Merge branch 'pyscf:master' into dev3

bytedance · Nov 13, 2023 · d5d4f33 · d5d4f33
2 parents 09010c1 + 5811d24
commit d5d4f33
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Showing 29 changed files with 658 additions and 140 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,7 @@
 **/__pycache__
 *.so
+*.npz
+*.out
 *current_revision
 **/build
 **/launch_logs
@@ -13,6 +15,7 @@ output/
 *.swo
 *.swp
 *~
+**/qchem_input.in
 #*
 dockerfiles/manylinux/wheelhouse
 gpu4pyscf/lib/bin

diff --git a/benchmarks/df/dft_driver.py b/benchmarks/df/dft_driver.py
@@ -3,6 +3,7 @@
 import pyscf
 import time
 import argparse
+import numpy as np
 from pyscf import lib
 from pyscf.dft import rks
 
@@ -41,18 +42,19 @@
     output_file = 'PySCF-16-cores-CPU.csv'
 output_file = args.output_path + output_file
 
-def run_dft(filename):
-    mol = pyscf.M(atom=filename, basis=bas, max_memory=64000)
+def run_dft(path, filename):
+    mol = pyscf.M(atom=path+filename, basis=bas, max_memory=64000)
     start_time = time.time()
     # set verbose >= 6 for debugging timer
-    mol.verbose = 4 #verbose
+    mol.verbose = 1 #verbose
     mol.max_memory = 40000
     mf = rks.RKS(mol, xc=xc).density_fit(auxbasis='def2-universal-jkfit')
     if args.solvent:
         mf = mf.PCM()
-        mf.lebedev_order = 29
-        mf.method = 'IEF-PCM'
-
+        mf.with_solvent.lebedev_order = 29
+        mf.with_solvent.method = 'IEF-PCM'
+        mf.with_solvent.eps = 78.3553
+    mf.verbose = 6
     mf.grids.atom_grid = (99,590)
     mf.chkfile = None
     prep_time = time.time() - start_time
@@ -62,7 +64,7 @@ def run_dft(filename):
     try:
         e_dft = mf.kernel()
         scf_time = time.time() - start_time
-    except:
+    except Exception:
         scf_time = -1
         e_dft = 0
 
@@ -76,25 +78,28 @@ def run_dft(filename):
         g.auxbasis_response = True
         f = g.kernel()
         grad_time = time.time() - start_time
-    except:
+    except Exception:
         grad_time = -1
+        f = -1
 
     # calculate hessian
     if args.device == 'GPU':
         cupy.get_default_memory_pool().free_all_blocks()
 
     hess_time = -1
     if args.with_hessian:
-        try:
-            start_time = time.time()
-            h = mf.Hessian()
-            h.auxbasis_response = 1
-            h.max_memory = 40000
-            hess = h.kernel()
-            hess_time = time.time() - start_time
-        except:
-            hess_time = -1
+        #try:
+        start_time = time.time()
+        h = mf.Hessian()
+        h.auxbasis_response = 1
+        h.max_memory = 40000
+        hess = h.kernel().reshape([3*mol.natm, 3*mol.natm])
+        hess_time = time.time() - start_time
+        #except Exception:
+        #   hess_time = -1
+        #    hess = -1
 
+    np.savez(args.output_path+filename+'.npz', e_dft=e_dft, grad=f, hess=hess)
     return mol.natm, mol.nao, scf_time, grad_time, hess_time, e_dft
 
 fields = ['mol','natm', 'nao', 't_scf', 't_gradient', 't_hessian', 'e_tot']
@@ -105,7 +110,7 @@ def run_dft(filename):
 for filename in sorted(os.listdir(args.input_path)):
     if filename.endswith(".xyz"):
         print(f'running DFT {filename}')
-        info = run_dft(args.input_path+filename)
+        info = run_dft(args.input_path, filename)
         row = [filename[:-4]]+list(info)
         csvwriter.writerow(row)
         csvfile.flush()

diff --git a/benchmarks/df/organic/basis/sto-3g/Tesla V100-SXM2-32GB.csv b/benchmarks/df/organic/basis/sto-3g/Tesla V100-SXM2-32GB.csv
@@ -1,14 +1,14 @@
 mol,natm,nao,t_scf,t_gradient,t_hessian,e_tot
-020_Vitamin_C,20,68,7.735399961471558,0.8264245986938477,-1,-675.5191427445513
-031_Inosine,31,107,12.40164589881897,1.2864620685577393,-1,-970.3601703535105
-033_Bisphenol_A,33,101,9.470605850219727,1.3010294437408447,-1,-722.4575094545307
-037_Mg_Porphin,37,141,10.585906982421875,1.7864344120025635,-1,-1173.7927754921361
-042_Penicillin_V,42,142,14.566765546798706,1.8530471324920654,-1,-1485.4649683739317
-045_Ochratoxin_A,45,157,16.409618377685547,2.151444673538208,-1,-1643.4719863900054
-052_Cetirizine,52,164,16.940945386886597,2.433612108230591,-1,-1591.0513291828825
-057_Tamoxifen,57,169,17.164642333984375,2.5976877212524414,-1,-1123.9167963056734
-066_Raffinose,66,202,19.061853408813477,3.485790491104126,-1,-1882.9880554750498
-084_Sphingomyelin,84,220,70.13539099693298,4.33745265007019,-1,-1787.52705174446
-095_Azadirachtin,95,299,35.65800380706787,7.805527210235596,-1,-2530.024523612371
-113_Taxol,113,361,41.06178140640259,12.37047815322876,-1,-2891.8561844202995
-168_Valinomycin,168,480,66.3832175731659,26.61207914352417,-1,-3744.922364373644
+020_Vitamin_C,20,68,7.868626832962036,1.0551254749298096,160.80799293518066,-675.538636198446
+031_Inosine,31,107,13.161744117736816,1.6693317890167236,409.3673324584961,-970.3940011476416
+033_Bisphenol_A,33,101,11.190348148345947,1.703892707824707,454.6797456741333,-722.4680797386372
+037_Mg_Porphin,37,141,13.220695495605469,2.3627896308898926,613.8060190677643,-1173.8015084893464
+042_Penicillin_V,42,142,16.221434831619263,2.5661509037017822,806.1365261077881,-1485.48745890511
+045_Ochratoxin_A,45,157,17.118950366973877,2.869781255722046,942.4001016616821,-1643.4889926123333
+052_Cetirizine,52,164,18.82169008255005,3.2975871562957764,1308.8825283050537,-1591.0707662509653
+057_Tamoxifen,57,169,20.3020281791687,3.712913751602173,1614.187731742859,-1123.9277518506542
+066_Raffinose,66,202,22.84470796585083,4.8171586990356445,2398.439987182617,-1883.0349428068212
+084_Sphingomyelin,84,220,35.961305141448975,-1,-1,-1787.6089723002701
+095_Azadirachtin,95,299,41.4524290561676,10.98064112663269,-1,-2530.0502561379244
+113_Taxol,113,361,56.471648931503296,-1,-1,-2891.887299140597
+168_Valinomycin,168,480,-1,-1,-1,0
diff --git a/benchmarks/df/organic/solvent/def2-tzvpp/Tesla V100-SXM2-32GB.csv b/benchmarks/df/organic/solvent/def2-tzvpp/Tesla V100-SXM2-32GB.csv
@@ -0,0 +1,9 @@
+mol,natm,nao,t_scf,t_gradient,t_hessian,e_tot
+020_Vitamin_C,20,484,10.453456163406372,2.7370195388793945,363.0008842945099,-685.0347463979249
+031_Inosine,31,757,20.68114447593689,6.736889600753784,1316.5888483524323,-983.7176439065447
+033_Bisphenol_A,33,751,17.637565851211548,6.877225160598755,1420.3841083049774,-731.960347742662
+037_Mg_Porphin,37,944,24.36361074447632,11.089943408966064,2439.1287682056427,-1188.8981396236977
+042_Penicillin_V,42,1007,30.862167358398438,11.582371473312378,3181.5790650844574,-1504.6450542609673
+045_Ochratoxin_A,45,1100,33.41982841491699,14.166359901428223,4029.220572948456,-1664.4396913351384
+052_Cetirizine,52,1198,40.039607763290405,18.70956540107727,6276.552805900574,-1611.0213497063874
+057_Tamoxifen,57,1274,44.171112298965454,20.529136180877686,7396.354176044464,-1138.3891845703356
diff --git a/benchmarks/df/organic/solvent/sto-3g/Tesla V100-SXM2-32GB.csv b/benchmarks/df/organic/solvent/sto-3g/Tesla V100-SXM2-32GB.csv
@@ -0,0 +1,7 @@
+mol,natm,nao,t_scf,t_gradient,t_hessian,e_tot
+020_Vitamin_C,20,68,7.757320165634155,1.040503740310669,174.4666724205017,-675.5386361984456
+031_Inosine,31,107,13.179906129837036,1.6433496475219727,417.5237069129944,-970.3940011476411
+033_Bisphenol_A,33,101,11.242647647857666,1.7435667514801025,456.6348719596863,-722.4680797386372
+037_Mg_Porphin,37,141,13.297797203063965,2.399493455886841,637.2147407531738,-1173.8015084893468
+042_Penicillin_V,42,142,17.28551435470581,2.550989866256714,803.3315801620483,-1485.4874589051096
+045_Ochratoxin_A,45,157,16.84193205833435,2.799733877182007,933.1838977336884,-1643.4889926123315
diff --git a/benchmarks/df/organic/xc/LDA/qchem-32-cores-cpu.csv b/benchmarks/df/organic/xc/LDA/qchem-32-cores-cpu.csv
@@ -1,13 +1 @@
 mol,t_scf,t_gradient,e_tot
-020_Vitamin_C,14.0,3.56,-679.7314745086
-031_Inosine,49.0,7.96,-975.8114577115
-033_Bisphenol_A,46.0,8.89,-725.553763622
-037_Mg_Porphin,66.0,14.14,-1179.2748793144
-042_Penicillin_V,64.0,13.64,-1494.103579632
-045_Ochratoxin_A,94.0,17.73,-1652.8352834053
-052_Cetirizine,141.0,23.98,-1599.5921033435
-057_Tamoxifen,130.0,28.07,-1128.1503311128
-066_Raffinose,159.0,38.63,-1894.4283011989
-084_Sphingomyelin,181.0,37.76,-1796.8793820306
-095_Azadirachtin,503.0,108.83,-2543.5362671667
-113_Taxol,815.0,175.2,-2906.2707301461
diff --git a/benchmarks/df/qchem.py b/benchmarks/df/qchem.py
@@ -8,6 +8,7 @@
 parser.add_argument('--xc',          type=str, default='B3LYP')
 parser.add_argument('--input_path',  type=str, default='./')
 parser.add_argument('--output_path', type=str, default='./')
+
 args = parser.parse_args()
 bas = args.basis
 xc = args.xc
@@ -43,9 +44,9 @@ def run_dft(filename):
         input.write("THRESH        14\n")
         input.write("BASIS_LIN_DEP_THRESH 12\n")
         input.write("$end\n")
-    
+
     filename = args.xc + '_' + args.basis
-    subprocess.run(['qchem', '-np', '32', 'qchem_input.in', filename])
+    subprocess.run(['qchem', '-save', '-np', '32', 'qchem_input.in', filename, args.output_path+'/qcarchive_'+filename])
     with open(filename, 'w') as output_file:
         lines = output_file.readlines()
         for line in lines:

diff --git a/benchmarks/df/qchem_input.in b/benchmarks/df/qchem_input.in
@@ -0,0 +1,86 @@
+$molecule
+0 1
+C                 -1.42958937   -1.01658249    2.44831265
+C                 -1.54149463   -0.27943595    1.12935913
+C                 -2.95243912    1.47129501    2.22492550
+C                 -2.84134324    0.73400280    3.54388810
+C                 -1.55797242   -0.06742235    3.62210684
+H                 -0.66497820    0.41085733    1.01283439
+H                 -0.44314689   -1.54644194    2.49994231
+H                 -3.93813646    2.00251835    2.17350554
+H                 -3.71865156    0.04459988    3.66018043
+H                 -0.68133448    0.63238265    3.63327796
+O                 -1.92499204    2.46279929    2.14636482
+C                 -1.46076301    4.67520648    3.08258818
+C                 -1.65192906    4.60593616    4.58432062
+H                 -0.74117334    5.43388332    2.85565168
+C                 -3.37658473    6.27667868    2.91318631
+C                 -2.26541279    5.88367074    5.11970508
+H                 -2.31747310    3.73866848    4.83580579
+C                 -3.56636040    6.20921206    4.41472333
+H                 -4.36600055    6.45426127    2.41719619
+H                 -1.54350069    6.73075622    4.97913735
+H                 -4.32958469    5.42429404    4.65913754
+O                 -2.52952388    7.38269576    2.59051909
+C                 -3.31900286    8.44866624    2.05635630
+C                 -3.26458455    9.66301263    2.97202724
+C                 -2.80523815   10.85434814    2.14390783
+H                 -4.26911658    9.86120175    3.42267320
+C                 -2.45049436   10.34868118    0.75291070
+H                 -1.92149828   11.34764146    2.62047963
+H                 -3.01626404   10.91739387   -0.02697788
+C                 -4.76356005    7.92754855    1.94107026
+H                 -4.78266313    7.06714393    1.30527236
+H                 -5.12531018    7.66145994    2.91227245
+O                 -2.82580898    0.52071700    1.05150767
+C                 -0.93849427    3.31732760    2.57761263
+H                 -0.77727115    3.36776157    1.52103158
+H                 -0.01653199    3.08491476    3.06839754
+C                 -1.49224313   -1.28985314   -0.03177454
+H                 -0.58145107   -1.84899344    0.02037852
+H                 -2.32526415   -1.95746693    0.04080516
+C                 -0.95163774   10.56175833    0.47072820
+H                 -0.66603955    9.99216789   -0.38886496
+H                 -0.38034325   10.24135666    1.31681648
+O                 -1.55044662   -0.58860344   -1.27666860
+H                 -1.40118565   -1.20385620   -1.99832308
+O                 -2.45542951   -2.00981905    2.52598600
+H                 -2.07814582   -2.83668451    2.83509848
+O                 -1.53066740   -0.81010098    4.84381994
+H                 -0.61998842   -0.98424670    5.09269150
+O                 -2.88646987    1.67226139    4.62209700
+H                 -3.42291955    1.31644411    5.33428785
+O                 -0.39050984    4.37790095    5.21813565
+H                 -0.43907755    4.65272412    6.13667438
+O                 -2.50206790    5.74947404    6.52358741
+H                 -2.24542728    6.55931660    6.97067871
+O                 -4.06906224    7.46048270    4.89065678
+H                 -4.76357327    7.30283533    5.53439721
+O                 -2.76235824    4.99928466    2.37789525
+O                 -5.59594331    8.94915410    1.38576835
+H                 -6.48998576    8.61436213    1.28476127
+O                 -2.79571817    8.86766013    0.68976834
+O                 -2.35757225    9.42976003    4.05268533
+H                 -2.22828280   10.24429373    4.54402949
+O                 -3.84292711   11.83519815    2.06622328
+H                 -3.45759742   12.71343457    2.10890596
+O                 -0.70503591   11.94904429    0.22675035
+H                  0.04258943   12.04182451   -0.36826913
+
+$end
+$rem
+JOBTYPE force
+METHOD LDA
+BASIS def2-tzvpp
+SYMMETRY      FALSE
+SYM_IGNORE    TRUE
+XC_GRID       000099000590
+NL_GRID       000050000194
+MAX_SCF_CYCLES 100
+ri_j        True
+ri_k        True
+aux_basis     RIJK-def2-tzvp
+SCF_CONVERGENCE 9
+THRESH        14
+BASIS_LIN_DEP_THRESH 12
+$end
diff --git a/benchmarks/df/run_gpu4pyscf.sh b/benchmarks/df/run_gpu4pyscf.sh
@@ -2,16 +2,23 @@
 
 DIR="./organic/xc"
 [ ! -d "$DIR" ] && mkdir -p "$DIR"
-for xc in LDA PBE B3LYP M06 wB97m-v
-do
-    python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/xc/$xc/ --xc $xc
-done
-exit
+
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/xc/LDA/ --xc LDA
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/xc/PBE/ --xc PBE
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/xc/B3LYP/ --xc B3LYP
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/xc/M06/ --xc M06
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/xc/wB97m-v/ --xc wB97m-v
 
 DIR="./organic/basis"
 [ ! -d "$DIR" ] && mkdir -p "$DIR"
 
-for basis in def2-svp def2-tzvpp def2-tzvpd sto-3g 6-31g
-do
-    python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/basis/$basis/ --basis $basis
-done
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/basis/def2-svp/ --basis def2-svp
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/basis/def2-tzvpp/ --basis def2-tzvpp
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/basis/def2-tzvpd/ --basis def2-tzvpd
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/basis/sto-3g/ --basis sto-3g
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/basis/6-31g/ --basis 6-31g
+
+DIR="./organic/solvent"
+[ ! -d "$DIR" ] && mkdir -p "$DIR"
+
+run --cpu 64 --memory 128 --gpu 1 -- python3 dft_driver.py --input_path ../molecules/organic/ --output_path ./organic/solvent/def2-tzvpp/ --basis def2-tzvpp --with_hessian True --solvent C-PCM
diff --git a/benchmarks/df/run_qchem.sh b/benchmarks/df/run_qchem.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 
+export QCSCRATCH=/tmp/
+
 DIR="./organic/xc"
 [ ! -d "$DIR" ] && mkdir -p "$DIR"
 
@@ -8,9 +10,9 @@ DIR="./organic/basis"
 
 #for xc in LDA PBE B3LYP M06 wB97m-v
 run --cpu 64 --memory 128 --gpu 0 -- python3 qchem.py --input_path ../molecules/organic/ --output_path ./organic/xc/LDA/ --xc LDA &&
-run --cpu 64 --memory 128 --gpu 0 -- python3 qchem.py --input_path ../molecules/organic/ --output_path ./organic/xc/PBE/ --xc PBE && 
+run --cpu 64 --memory 128 --gpu 0 -- python3 qchem.py --input_path ../molecules/organic/ --output_path ./organic/xc/PBE/ --xc PBE &&
 run --cpu 64 --memory 128 --gpu 0 -- python3 qchem.py --input_path ../molecules/organic/ --output_path ./organic/xc/B3LYP/ --xc B3LYP &&
-run --cpu 64 --memory 128 --gpu 0 -- python3 qchem.py --input_path ../molecules/organic/ --output_path ./organic/xc/M06/ --xc M06 && 
+run --cpu 64 --memory 128 --gpu 0 -- python3 qchem.py --input_path ../molecules/organic/ --output_path ./organic/xc/M06/ --xc M06 &&
 run --cpu 64 --memory 128 --gpu 0 -- python3 qchem.py --input_path ../molecules/organic/ --output_path ./organic/xc/wB97m-v/ --xc wB97m-v &&
 
 #for basis in def2-svp def2-tzvpp def2-tzvpd sto-3g 6-31g 6-31g*

diff --git a/benchmarks/scf/dft_driver.py b/benchmarks/scf/dft_driver.py
@@ -15,7 +15,10 @@
 parser.add_argument('--device',       type=str, default='GPU')
 parser.add_argument('--input_path',   type=str, default='./')
 parser.add_argument('--output_path',  type=str, default='./')
+parser.add_argument('--with_gradient', type=bool, default=False)
 parser.add_argument('--with_hessian', type=bool, default=False)
+parser.add_argument("--solvent",  type=bool, default=False)
+
 args = parser.parse_args()
 bas = args.basis
 verbose = args.verbose
@@ -39,23 +42,29 @@
     output_file = 'PySCF-16-cores-CPU.csv'
 output_file = args.output_path + output_file
 
-def run_dft(filename):  
+def run_dft(filename):
     mol = pyscf.M(atom=filename, basis=bas, max_memory=64000)
-    start_time = time.time()  
+    start_time = time.time()
     # set verbose >= 6 for debugging timer
     mol.verbose = 4 #verbose
     mol.max_memory = 40000
     mf = rks.RKS(mol, xc=xc)
+    if args.solvent:
+        mf = mf.PCM()
+        mf.with_solvent.lebedev_order = 29
+        mf.with_solvent.method = 'IEF-PCM'
+        mf.with_solvent.eps = 78.3553
     mf.grids.atom_grid = (99,590)
     mf.chkfile = None
     prep_time = time.time() - start_time
     mf.conv_tol = 1e-9
     mf.nlcgrids.atom_grid = (50,194)
     mf.max_cycle = 100
+    print(mf.scf_summary)
     try:
         e_dft = mf.kernel()
         scf_time = time.time() - start_time
-    except:
+    except Exception:
         scf_time = -1
         e_dft = 0
 
@@ -68,13 +77,13 @@ def run_dft(filename):
         g.max_memory = 40000
         f = g.kernel()
         grad_time = time.time() - start_time
-    except:
+    except Exception:
         grad_time = -1
 
     # calculate hessian
     if args.device == 'GPU':
         cupy.get_default_memory_pool().free_all_blocks()
-    
+
     hess_time = -1
     if args.with_hessian:
         try:
@@ -83,7 +92,7 @@ def run_dft(filename):
             h.max_memory = 40000
             hess = h.kernel()
             hess_time = time.time() - start_time
-        except:
+        except Exception:
             hess_time = -1
 
     return mol.natm, mol.nao, scf_time, grad_time, hess_time, e_dft