Bugfix v0.6.9 (#63)

* save * implement SMD solvent model * updated readme * fixed issues after v0.6.9 * format examples * output = /dev/null in test_smd.py
pyscf · Dec 12, 2023 · 94c26ff · 94c26ff
1 parent c818905
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diff --git a/examples/00-h2o.py b/examples/00-h2o.py
@@ -18,15 +18,15 @@
 from gpu4pyscf.dft import rks
 lib.num_threads(8)
 
-atom ='''
+atom = '''
 O       0.0000000000    -0.0000000000     0.1174000000
 H      -0.7570000000    -0.0000000000    -0.4696000000
 H       0.7570000000     0.0000000000    -0.4696000000
 '''
 
-xc='B3LYP'
-bas='def2-tzvpp'
-auxbasis='def2-tzvpp-jkfit'
+xc = 'B3LYP'
+bas = 'def2-tzvpp'
+auxbasis = 'def2-tzvpp-jkfit'
 scf_tol = 1e-10
 max_scf_cycles = 50
 screen_tol = 1e-14

diff --git a/examples/01-h2o_dftd3.py b/examples/01-h2o_dftd3.py
@@ -27,9 +27,9 @@
 H       0.7570000000     0.0000000000    -0.4696000000
 '''
 
-xc='B3LYP'
-bas='def2-tzvpp'
-auxbasis='def2-tzvpp-jkfit'
+xc = 'B3LYP'
+bas = 'def2-tzvpp'
+auxbasis = 'def2-tzvpp-jkfit'
 scf_tol = 1e-10
 max_scf_cycles = 50
 screen_tol = 1e-14

diff --git a/examples/02-h2o_geomopt.py b/examples/02-h2o_geomopt.py
@@ -13,22 +13,23 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+import time
 import pyscf
 from pyscf import lib
 from pyscf.geomopt.geometric_solver import optimize
 from gpu4pyscf.dft import rks
 
 lib.num_threads(8)
 
-atom =''' 
+atom = '''
 O       0.0000000000    -0.0000000000     0.1174000000
 H      -0.7570000000    -0.0000000000    -0.4696000000
 H       0.7570000000     0.0000000000    -0.4696000000
 '''
 
-xc='B3LYP'
-bas='def2-tzvpp'
-auxbasis='def2-tzvpp-jkfit'
+xc = 'B3LYP'
+bas = 'def2-tzvpp'
+auxbasis = 'def2-tzvpp-jkfit'
 scf_tol = 1e-10
 max_scf_cycles = 50
 screen_tol = 1e-14
@@ -46,7 +47,6 @@
 def callback(envs):
     gradients.append(envs['gradients'])
 
-import time
 start_time = time.time()
 mol_eq = optimize(mf_GPU, maxsteps=20, callback=callback)
 print("Optimized coordinate:")

diff --git a/examples/03-h2o_dzvp.py b/examples/03-h2o_dzvp.py
@@ -25,8 +25,8 @@
 H       0.7570000000     0.0000000000    -0.4696000000
 '''
 
-xc='B3LYP'
-bas='dzvp'
+xc = 'B3LYP'
+bas = 'dzvp'
 scf_tol = 1e-10
 max_scf_cycles = 50
 screen_tol = 1e-1

diff --git a/examples/05-h2o_multipole.py b/examples/05-h2o_multipole.py
@@ -16,7 +16,7 @@
 import pyscf
 from gpu4pyscf.dft import rks
 
-atom =''' 
+atom ='''
 O       0.0000000000    -0.0000000000     0.1174000000
 H      -0.7570000000    -0.0000000000    -0.4696000000
 H       0.7570000000     0.0000000000    -0.4696000000
@@ -26,8 +26,12 @@
 mol.verbose = 1
 mf = rks.RKS(mol, xc='B3LYP').density_fit(auxbasis='def2-tzvpp-jkfit')
 mf.kernel()
+dm = mf.make_rdm1()
 
-dip = mf.dip_moment(unit='DEBYE')
+dip = mf.dip_moment(unit='DEBYE', dm=dm.get())
+print('dipole moment:')
 print(dip)
-quad = mf.quad_moment(unit='DEBYE-ANG')
+
+quad = mf.quad_moment(unit='DEBYE-ANG', dm=dm.get())
+print('quadrupole moment:')
 print(quad)
diff --git a/examples/07-transition_state.py b/examples/07-transition_state.py
@@ -47,9 +47,9 @@
    H          1.06461        2.50818       -0.45885'''
 
 
-xc='B3LYP'
-bas='def2-tzvpp'
-auxbasis='def2-tzvpp-jkfit'
+xc = 'B3LYP'
+bas = 'def2-tzvpp'
+auxbasis = 'def2-tzvpp-jkfit'
 scf_tol = 1e-10
 max_scf_cycles = 50
 screen_tol = 1e-14

diff --git a/examples/09-mbis.py b/examples/09-mbis.py
@@ -25,9 +25,9 @@
 H       0.7570000000     0.0000000000    -0.4696000000
 '''
 
-xc='B3LYP'
-bas='def2-tzvpp'
-auxbasis='def2-tzvpp-jkfit'
+xc = 'B3LYP'
+bas = 'def2-tzvpp'
+auxbasis = 'def2-tzvpp-jkfit'
 scf_tol = 1e-10
 max_scf_cycles = 50
 screen_tol = 1e-14

diff --git a/examples/10-ecp.py b/examples/10-ecp.py
@@ -17,16 +17,15 @@
 from gpu4pyscf.dft import rks
 
 atom = '''
-I 0 0 0 
+I 0 0 0
 I 1 0 0
 '''
-bas='def2-qzvpp'
+bas = 'def2-qzvpp'
 grids_level = 6
 
 mol = pyscf.M(atom=atom, basis=bas, ecp=bas)
 mol.verbose = 1
 
 mf = rks.RKS(mol, xc='b3lyp')
 mf.grids.level = grids_level
-mf.device = 'gpu'
 e_dft = mf.kernel()
diff --git a/examples/11-nlc.py b/examples/11-nlc.py
@@ -20,7 +20,7 @@
 from gpu4pyscf.dft import rks
 lib.num_threads(8)
 
-atom =''' 
+atom ='''
 O       0.0000000000    -0.0000000000     0.1174000000
 H      -0.7570000000    -0.0000000000    -0.4696000000
 H       0.7570000000     0.0000000000    -0.4696000000

diff --git a/examples/15-chelpg.py b/examples/15-chelpg.py
@@ -35,4 +35,5 @@
 mf.grids.level = 5
 mf.kernel()
 q = chelpg.eval_chelpg_layer_gpu(mf)
+print('partial charge with CHELPG')
 print(q) # [ 0.04402311  0.11333945 -0.25767919  0.10031663]
diff --git a/examples/16-smd.py b/examples/16-smd.py
@@ -35,4 +35,4 @@
 mf.with_solvent.method = 'SMD'
 mf.with_solvent.solvent = 'water'
 e_tot = mf.kernel()
-print(e_tot)
+print('total energy with SMD:', e_tot)
diff --git a/examples/17-to_gpu.py b/examples/17-to_gpu.py
@@ -0,0 +1,57 @@
+# Copyright 2023 The GPU4PySCF Authors. All Rights Reserved.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import pyscf
+from pyscf import lib
+from pyscf.dft import rks
+lib.num_threads(8)
+
+atom = '''
+O       0.0000000000    -0.0000000000     0.1174000000
+H      -0.7570000000    -0.0000000000    -0.4696000000
+H       0.7570000000     0.0000000000    -0.4696000000
+'''
+
+xc = 'B3LYP'
+bas = 'sto3g'
+scf_tol = 1e-10
+max_scf_cycles = 50
+screen_tol = 1e-14
+grids_level = 3
+
+mol = pyscf.M(atom=atom, basis=bas, max_memory=32000, output='./pyscf.log')
+
+mol.verbose = 4
+mf = rks.RKS(mol, xc=xc).density_fit()
+mf_GPU = mf.to_gpu()
+mf_GPU.grids.level = grids_level
+mf_GPU.conv_tol = scf_tol
+mf_GPU.max_cycle = max_scf_cycles
+mf_GPU.screen_tol = screen_tol
+
+# Compute Energy
+e_dft = mf_GPU.kernel()
+print(f"total energy = {e_dft}")
+
+# Compute Gradient
+g = mf_GPU.nuc_grad_method()
+g.max_memory = 20000
+g.auxbasis_response = True
+g_dft = g.kernel()
+
+# Compute Hessian
+h = mf_GPU.Hessian()
+h.auxbasis_response = 2
+h_dft = h.kernel()
diff --git a/gpu4pyscf/df/df_jk.py b/gpu4pyscf/df/df_jk.py
@@ -123,6 +123,8 @@ class _DFHF(df_jk._DFHF):
 
     from gpu4pyscf.lib.utils import to_cpu, to_gpu, device
 
+    _keys = {'rhoj', 'rhok', 'disp', 'screen_tol'}
+
     def __init__(self, mf, dfobj, only_dfj):
         self.__dict__.update(mf.__dict__)
         self._eri = None

diff --git a/gpu4pyscf/df/int3c2e.py b/gpu4pyscf/df/int3c2e.py
@@ -1409,7 +1409,7 @@ def sort_mol(mol0, cart=True):
     # Sort basis according to angular momentum and contraction patterns so
     # as to group the basis functions to blocks in GPU kernel.
     '''
-    mol = copy.copy(mol0)
+    mol = mol0.copy(deep=True)
     l_ctrs = mol._bas[:,[gto.ANG_OF, gto.NPRIM_OF]]
 
     uniq_l_ctr, _, inv_idx, l_ctr_counts = np.unique(

diff --git a/gpu4pyscf/solvent/tests/test_smd.py b/gpu4pyscf/solvent/tests/test_smd.py
@@ -28,7 +28,7 @@ def setUpModule():
 H       0.7570000000     0.0000000000    -0.4696000000
     '''
     mol.basis = 'def2-tzvpp'
-    #mol.output = '/dev/null'
+    mol.output = '/dev/null'
     mol.build()
     lebedev_order = 29