Merge master

.github/workflows/ci.yaml

@@ -8,7 +8,7 @@ on:
     - cron: '0 2 * * *'
 
 jobs:
-  build:
+  full:
     name: python ${{ matrix.python-version }} on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
 
@@ -19,6 +19,7 @@ jobs:
           - {python-version: "3.8", os: ubuntu-latest, documentation: True}
           - {python-version: "3.9", os: ubuntu-latest, documentation: False}
           - {python-version: "3.10", os: ubuntu-latest, documentation: False}
+          - {python-version: "3.11", os: ubuntu-latest, documentation: False}
 
     steps:
       - uses: actions/checkout@v2
@@ -33,8 +34,12 @@ jobs:
         run: |
           python -m pip install wheel --user
           python -m pip install setuptools --upgrade --user
+<<<<<<< HEAD
           python -m pip install https://github.com/BoothGroup/dyson/archive/master.zip
           python -m pip install .[dmet] --user
+=======
+          python -m pip install .[dmet,ebcc] --user
+>>>>>>> master
       - name: Run unit tests
         run: |
           python -m pip install pytest pytest-cov --user
@@ -61,3 +66,29 @@ jobs:
           force_orphan: true
         if: ${{ matrix.documentation && github.ref == 'refs/heads/master' && github.event_name != 'schedule' }}
 
+  bare:
+    name: python 3.8 on ubuntu-latest with no optional dependencies
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Upgrade pip
+        run: |
+          python -m pip install --upgrade pip
+      - name: Install Vayesta
+        run: |
+          python -m pip install wheel --user
+          python -m pip install setuptools --upgrade --user
+          python -m pip install . --user
+      - name: Run unit tests
+        run: |
+          python -m pip install pytest pytest-cov --user
+          python .github/workflows/run_tests.py
+

.github/workflows/run_tests.py

@@ -1,6 +1,6 @@
 import pytest
-import sys
 import os
+import sys
 
 src = os.path.abspath(os.path.join(__file__, "..", "..", "..", "vayesta"))
 

MANIFEST.in

@@ -1,11 +1,13 @@
 include MANIFEST.in
-include README.md setup.py CHANGELOG LICENSE
+include README.md pyproject.toml setup.py CHANGELOG LICENSE
 
 global-exclude *.py[cod]
 prune vayesta/libs/build
 
 recursive-include vayesta *.dat
+recursive-include vayesta/misc/gmtkn55 *
 include vayesta/libs/*.so
+include vayesta/logo.txt
 
 # MacOS dynamic libraries
 include vayesta/libs/*.dylib

examples/dmet/02-rotational-symmetry.py

@@ -27,7 +27,7 @@
 # One-shot DMET
 dmet = vayesta.dmet.DMET(mf, solver='FCI', maxiter=1)
 with dmet.sao_fragmentation() as f:
-    with f.rotational_symmetry(3, axis='z'):
+    with f.rotational_symmetry(3, axis=[0,0,1]):
         f.add_atomic_fragment([0,1])
 dmet.kernel()
 

examples/dmet/04-h-ring-diis.py

@@ -1,5 +1,8 @@
 import numpy as np
 
+import pyscf
+import pyscf.scf 
+
 import vayesta
 import vayesta.dmet
 from vayesta.misc.molecules import ring

examples/dmet/63-hubbard-1d.py

@@ -20,6 +20,7 @@
         f.add_atomic_fragment(list(range(site, site+nimp)))
 dmet.kernel()
 
+print(dmet.fragments)
 # Calculate a single fragment and use translational symmetry:
 dmet_sym = vayesta.dmet.DMET(mf, solver='FCI')
 # Specify the number of translational copies in direction of the three lattice vectors by passing a list with three

examples/edmet/01-1d-hubbard-comparison.py

@@ -24,7 +24,7 @@ def gen_comparison(hubbard_u, nimp=2):
         mf = gen_hub(nsite, hubbard_u)
 
         dmet = vayesta.dmet.DMET(mf, solver='FCI', charge_consistent=True, maxiter=1,
-                                 bath_type=None)
+                                 bath_options=dict(bathtype='dmet'))
         with dmet.site_fragmentation() as f:
             frag = f.add_atomic_fragment(list(range(nimp)))
         # Add fragments which are translationally symmetric to f - the results of the fragment f
@@ -33,7 +33,7 @@ def gen_comparison(hubbard_u, nimp=2):
         symfrags = frag.make_tsymmetric_fragments(tvecs=[nsite // nimp, 1, 1])
         res_dmet += [sum(dmet.fragments[0].get_dmet_energy_contrib())/nimp]
 
-        edmet = vayesta.edmet.EDMET(mf, solver="EBFCI", charge_consistent = True,maxiter=1, bath_type=None)
+        edmet = vayesta.edmet.EDMET(mf, solver="FCI", charge_consistent = True,maxiter=1, bath_options=dict(bathtype='dmet'))
         with edmet.site_fragmentation() as f:
             frag = f.add_atomic_fragment(list(range(nimp)))
         # Add fragments which are translationally symmetric to f - the results of the fragment f

examples/edmet/10-bosonic-Hamiltonians.py

@@ -15,17 +15,17 @@
 
 # Can generate bosons using either RPA couplings or direct projection of the Hamiltonian into the bosonic space.
 
-rdfedmet_drpa_bos = vayesta.edmet.EDMET(mf, solver="EBCCSD", dmet_threshold=1e-12, bosonic_interaction="direct", oneshot=True, make_dd_moments=False)
+rdfedmet_drpa_bos = vayesta.edmet.EDMET(mf, solver="CCSD-S-1-1", bath_options=dict(dmet_threshold=1e-12), bosonic_interaction="direct", oneshot=True, make_dd_moments=False)
 with rdfedmet_drpa_bos.iao_fragmentation() as f:
     f.add_all_atomic_fragments()
 rdfedmet_drpa_bos.kernel()
 
-rdfedmet_qba_directbos = vayesta.edmet.EDMET(mf, solver="EBCCSD", dmet_threshold=1e-12, bosonic_interaction="qba", oneshot=True, make_dd_moments=False)
+rdfedmet_qba_directbos = vayesta.edmet.EDMET(mf, solver="CCSD-S-1-1", bath_options=dict(dmet_threshold=1e-12), bosonic_interaction="qba", oneshot=True, make_dd_moments=False)
 with rdfedmet_qba_directbos.iao_fragmentation() as f:
     f.add_all_atomic_fragments()
 rdfedmet_qba_directbos.kernel()
 
-rdfedmet_qba = vayesta.edmet.EDMET(mf, solver="EBCCSD", dmet_threshold=1e-12, bosonic_interaction="qba_bos_ex",
+rdfedmet_qba = vayesta.edmet.EDMET(mf, solver="CCSD-S-1-1", bath_options=dict(dmet_threshold=1e-12), bosonic_interaction="qba_bos_ex",
                                    oneshot=True, make_dd_moments=False)
 with rdfedmet_qba.iao_fragmentation() as f:
     f.add_all_atomic_fragments()

examples/edmet/30-start-from-dft.py

@@ -25,7 +25,7 @@
 # The KS opbject needs to be converted to a HF object:
 lda = lda.to_rhf()
 
-emb_lda = vayesta.edmet.EDMET(lda, dmet_threshold=1e-12, solver="EBCCSD", oneshot=True, make_dd_moments=False)
+emb_lda = vayesta.edmet.EDMET(lda, solver="CCSD-S-1-1", bath_options=dict(dmet_threshold=1e-12), oneshot=True, make_dd_moments=False)
 with emb_lda.iao_fragmentation() as f:
     f.add_all_atomic_fragments()
 emb_lda.kernel()
@@ -38,7 +38,7 @@
 # The KS opbject needs to be converted to a HF object:
 b3lyp = b3lyp.to_rhf()
 
-emb_b3lyp = vayesta.edmet.EDMET(b3lyp, dmet_threshold=1e-12, solver="EBCCSD", oneshot=True, make_dd_moments=False)
+emb_b3lyp = vayesta.edmet.EDMET(b3lyp, solver="CCSD-S-1-1", bath_options=dict(dmet_threshold=1e-12), oneshot=True, make_dd_moments=False)
 with emb_b3lyp.iao_fragmentation() as f:
     f.add_all_atomic_fragments()
 emb_b3lyp.kernel()
@@ -47,7 +47,7 @@
 hf = pyscf.scf.RHF(mol).density_fit()
 hf.kernel()
 
-emb_hf = vayesta.edmet.EDMET(hf, dmet_threshold=1e-12, solver="EBCCSD", oneshot=True, make_dd_moments=False)
+emb_hf = vayesta.edmet.EDMET(hf, solver="CCSD-S-1-1", bath_options=dict(dmet_threshold=1e-12), oneshot=True, make_dd_moments=False)
 with emb_hf.iao_fragmentation() as f:
     f.add_all_atomic_fragments()
 emb_hf.kernel()

examples/edmet/70-h-ring-benchmark.py → examples/edmet/70-h-ring-benchmark-df.py

@@ -8,12 +8,28 @@
 
 
 natom = 6
-filename = "energies_scEDMET_h{:d}_compare.txt".format(natom)
+filename = "energies_scEDMET_h{:d}_compare_df.txt".format(natom)
 
 with open(filename, "a") as f:
     f.write(("%6s" + "  %16s  " * 8) % (
     "d", "HF", "CCSD", "FCI", "DMET (Oneshot)", "DMET", "EDMET (Oneshot)", "EDMET (old)", "EDMET (new)"))
 
+import numpy as np
+import pyscf.cc
+import pyscf.fci
+import pyscf.tools
+import pyscf.tools.ring
+import vayesta.dmet
+import vayesta.edmet
+
+
+natom = 6
+filename = "energies_h{:d}_compare_df.txt".format(natom)
+
+with open(filename, "a") as f:
+    f.write(("%6s" + "  %16s  " * 6 + "\n") % (
+    "d", "HF", "CCSD", "FCI", "DMET (Oneshot)", "DMET", "EDMET (Oneshot)"))
+
 for d in np.arange(0.5, 3.0001, 0.25):
 
     ring = pyscf.tools.ring.make(natom, d)
@@ -27,7 +43,10 @@
     mol.build()
 
     # Hartree-Fock
-    mf = pyscf.scf.RHF(mol)
+    # Replace with
+    # mf = pyscf.scf.RHF(mol)
+    # to run without density fitting.
+    mf = pyscf.scf.RHF(mol).density_fit()
     mf.kernel()
 
     # Reference full system CCSD:
@@ -51,43 +70,26 @@
             f.add_atomic_fragment([i, i + 1])
     dmet_diis.kernel()
     # Single-shot EDMET
-    edmet_oneshot = vayesta.edmet.EDMET(mf, solver='EBFCI', max_elec_err=1e-4, maxiter=1, max_boson_occ=2)
+    edmet_oneshot = vayesta.edmet.EDMET(mf, solver='FCI', max_elec_err=1e-4, maxiter=1,
+                                        solver_options=dict(max_boson_occ=2), oneshot=True)
     with edmet_oneshot.iao_fragmentation() as f:
         for i in range(0, natom, 2):
             f.add_atomic_fragment([i, i + 1])
     edmet_oneshot.kernel()
-    # Full DMET
-    edmet_orig = vayesta.edmet.EDMET(mf, solver='EBFCI', charge_consistent=True, max_elec_err=1e-4, maxiter=40,
-                                     max_boson_occ=2, old_sc_condition=True)
-    with edmet_orig.iao_fragmentation() as f:
-        for i in range(0, natom, 2):
-            f.add_atomic_fragment([i, i + 1])
-    edmet_orig.kernel()
 
-    edmet_new = vayesta.edmet.EDMET(mf, solver='EBFCI', charge_consistent=True, max_elec_err=1e-4, maxiter=40,
-                                    max_boson_occ=2)
-    with edmet_new.iao_fragmentation() as f:
-        for i in range(0, natom, 2):
-            f.add_atomic_fragment([i, i + 1])
-    edmet_new.kernel()
-
-    e_sc_edmet1 = edmet_orig.e_tot if edmet_orig.converged else np.NaN
-    e_sc_edmet2 = edmet_new.e_tot if edmet_new.converged else np.NaN
     e_cc = mycc.e_tot if mycc.converged else np.NaN
     e_dmet = dmet_diis.e_tot if dmet_diis.converged else np.NaN
     print("E%-14s %+16.8f Ha" % ('(HF)=', mf.e_tot))
     print("E%-14s %+16.8f Ha" % ('(CCSD)=', e_cc))
     print("E%-14s %+16.8f Ha" % ('(FCI)=', myfci.e_tot))
     print("E%-14s %+16.8f Ha" % ('(DMET-FCI)=', dmet_oneshot.e_tot))
     print("E%-14s %+16.8f Ha" % ('(EDMET-FCI-Oneshot)=', edmet_oneshot.e_tot))
-    print("E%-14s %+16.8f Ha" % ('(EDMET1-FCI)=', e_sc_edmet1))
-    print("E%-14s %+16.8f Ha" % ('(EDMET2-FCI)=', e_sc_edmet2))
+
 
     with open(filename, "a") as f:
-        f.write("%.2f  % 16.8f  % 16.8f  % 16.8f  %16.8f  %16.8f  %16.8f  %16.8f  %16.8f\n" % (d, mf.e_tot, e_cc,
+        f.write("%.2f  % 16.8f  % 16.8f  % 16.8f  %16.8f  %16.8f  %16.8f\n" % (d, mf.e_tot, e_cc,
                                                                                                myfci.e_tot,
                                                                                                dmet_oneshot.e_tot,
                                                                                                e_dmet,
-                                                                                               edmet_oneshot.e_tot,
-                                                                                               e_sc_edmet1,
-                                                                                               e_sc_edmet2))
+                                                                                               edmet_oneshot.e_tot
+                                                                                               ))