Enhance green-kubo transport and refactor transport module (#97)

* update green-kubo transport and refactor transport module - `TransportAutoCorr` is renamed to `TransportKubo` and `ChargeTransport` is renamed to `ChargeDiffusionDynamics` for accuracy. - In `TransportKubo` the current operator are now automatically constructed from `MolList2`. - If Peielrs terms are present in the model `TransportKubo` will split the current operator into two parts and obtain 5 sets of autocorrelation functions in total. * rename `transport.py` in `example` * rename `ChargeTransport` in `./example/fmo.py` * fix several bugs
shuaigroup · Jul 2, 2020 · 8837a13 · 8837a13
1 parent 54cf9c1
commit 8837a13
Show file tree

Hide file tree

Showing 20 changed files with 643 additions and 343 deletions.
diff --git a/doc/source/ct.rst b/doc/source/ct.rst
@@ -1,13 +1,15 @@
 Charge Transport
 *************************************
 
-charge diffusion simulation
+Obtain mobility by Green-Kubo formula
+===============================
+.. automodule:: renormalizer.transport.kubo
+   :members:
+
+Charge diffusion simulation dynamics
 ===========================
-.. automodule:: renormalizer.transport.transport
+.. automodule:: renormalizer.transport.dynamics
    :members:
 
 
-obtain mobility by Kubo formula
-===============================
-.. automodule:: renormalizer.transport.autocorr
-   :members:
+
diff --git a/example/transport.py → example/dynamics.py b/example/transport.py → example/dynamics.py
@@ -9,8 +9,8 @@
 import yaml
 
 from renormalizer.model import load_from_dict
-from renormalizer.transport import ChargeTransport
-from renormalizer.utils import log, Quantity, EvolveConfig, EvolveMethod, RungeKutta, CompressConfig
+from renormalizer.transport import ChargeDiffusionDynamics
+from renormalizer.utils import log, EvolveConfig, EvolveMethod, CompressConfig
 
 logger = logging.getLogger(__name__)
 
@@ -27,15 +27,15 @@
     mol_list, temperature = load_from_dict(param, 3, False)
     compress_config = CompressConfig(max_bonddim=16)
     evolve_config = EvolveConfig(EvolveMethod.tdvp_ps, adaptive=True, guess_dt=2)
-    ct = ChargeTransport(
+    cdd = ChargeDiffusionDynamics(
         mol_list,
         temperature=temperature,
         compress_config=compress_config,
         evolve_config=evolve_config,
         rdm=False,
     )
-    ct.dump_dir = param["output dir"]
-    ct.job_name = param["fname"]
-    ct.custom_dump_info["comment"] = param["comment"]
-    ct.evolve(param.get("evolve dt"), param.get("nsteps"), param.get("evolve time"))
+    cdd.dump_dir = param["output dir"]
+    cdd.job_name = param["fname"]
+    cdd.custom_dump_info["comment"] = param["comment"]
+    cdd.evolve(param.get("evolve dt"), param.get("nsteps"), param.get("evolve time"))
     # ct.evolve(evolve_dt, 100, param.get("evolve time"))
diff --git a/example/fmo.py b/example/fmo.py
@@ -3,7 +3,7 @@
 from renormalizer.model import Phonon, Mol, MolList
 from renormalizer.utils import Quantity, EvolveConfig, CompressConfig, CompressCriteria, EvolveMethod
 from renormalizer.utils.constant import cm2au
-from renormalizer.transport import ChargeTransport, InitElectron
+from renormalizer.transport import ChargeDiffusionDynamics, InitElectron
 
 import numpy as np
 
@@ -157,7 +157,7 @@
     evolve_dt = 160
     evolve_config = EvolveConfig(EvolveMethod.tdvp_ps, guess_dt=evolve_dt)
     compress_config = CompressConfig(CompressCriteria.fixed, max_bonddim=32)
-    ct = ChargeTransport(mol_list, evolve_config=evolve_config, compress_config=compress_config, init_electron=InitElectron.fc)
+    ct = ChargeDiffusionDynamics(mol_list, evolve_config=evolve_config, compress_config=compress_config, init_electron=InitElectron.fc)
     ct.dump_dir = "./"
     ct.job_name = 'fmo'
     ct.stop_at_edge = False

diff --git a/example/run.sh b/example/run.sh
@@ -1,11 +1,11 @@
 export PYTHONPATH=../:PYTHONPATH
 code=0
-for python_args in fmo.py sbm.py h2o_qc.py "transport.py std.yaml" "transport_autocorr.py std.yaml"; do
+for python_args in fmo.py sbm.py h2o_qc.py "dynamics.py std.yaml" "transport_kubo.py std.yaml"; do
     echo ============================$python_args=============================
     timeout 20s python $python_args
     exit_code=$?
     echo ============================$python_args=============================
-    # the time out exit code or normal exit code
+    # if not the time out exit code or normal exit code
     if [ $exit_code -ne 124 ] && [ $exit_code -ne 0 ]; then
         echo "The script failed with exit code $exit_code" >&2
         code=1

diff --git a/example/transport_autocorr.py → example/transport_kubo.py b/example/transport_autocorr.py → example/transport_kubo.py
@@ -9,7 +9,7 @@
 import yaml
 
 from renormalizer.model import load_from_dict
-from renormalizer.transport import TransportAutoCorr
+from renormalizer.transport import TransportKubo
 from renormalizer.utils import log, Quantity, EvolveConfig, EvolveMethod, RungeKutta, CompressConfig, BondDimDistri
 
 logger = logging.getLogger(__name__)
@@ -28,9 +28,9 @@
     compress_config = CompressConfig(threshold=1e-4)
     ievolve_config = EvolveConfig(adaptive=True, guess_dt=temperature.to_beta() / 1000j)
     evolve_config = EvolveConfig(adaptive=True, guess_dt=2)
-    ct = TransportAutoCorr(mol_list, temperature=temperature, ievolve_config=ievolve_config,
-                           compress_config=compress_config, evolve_config=evolve_config, dump_dir=param["output dir"],
-                           job_name=param["fname"] + "_autocorr")
+    ct = TransportKubo(mol_list, temperature=temperature, ievolve_config=ievolve_config,
+                       compress_config=compress_config, evolve_config=evolve_config, dump_dir=param["output dir"],
+                       job_name=param["fname"] + "_autocorr")
     # ct.latest_mps.compress_add = True
     ct.evolve(param.get("evolve dt"), param.get("nsteps"), param.get("evolve time"))
     # ct.evolve(evolve_dt, 100, param.get("evolve time"))
diff --git a/renormalizer/model/mlist.py b/renormalizer/model/mlist.py
@@ -2,7 +2,7 @@
 # Author: Jiajun Ren <jiajunren0522@gmail.com>
 
 import copy
-from collections import OrderedDict
+from collections import OrderedDict, defaultdict
 from typing import List, Union, Dict
 from enum import Enum
 
@@ -489,6 +489,7 @@ def get_pure_dmrg_mollist(self):
 
     def mol_list2_para(self, formula="vibronic"):
         mol_list2 = MolList2.MolList_to_MolList2(self, formula)
+        self.multi_dof_basis = self.scheme == 4
         self.order = mol_list2.order
         self.basis = mol_list2.basis
         self.model = mol_list2.model
@@ -510,6 +511,7 @@ def rewrite_model(self, model, model_translator):
         mol_list_new.basis = self.basis
         mol_list_new.model = model
         mol_list_new.model_translator = model_translator
+        mol_list_new.multi_dof_basis = self.multi_dof_basis
         return mol_list_new
 
     def __getitem__(self, idx):
@@ -553,3 +555,33 @@ def load_from_dict(param, scheme, lam: bool):
                        j_constant, scheme=scheme
                        )
     return mol_list, temperature
+
+
+def vibronic_to_general(model):
+    new_model = defaultdict(list)
+    for e_k, e_v in model.items():
+        for kk, vv in e_v.items():
+            # it's difficult to rename `kk` because sometimes it's related to
+            # phonons sometimes it's `"J"`
+            if e_k == "I":
+                # operators without electronic dof, simple phonon
+                new_model[kk] = vv
+            else:
+                # operators with electronic dof
+                assert isinstance(e_k, tuple) and len(e_k) == 2
+                if e_k[0] == e_k[1]:
+                    # diagonal
+                    new_e_k = (e_k[0],)
+                    e_op = (Op(r"a^\dagger a", 0),)
+                else:
+                    # off-diagonal
+                    new_e_k = e_k
+                    e_op = (Op(r"a^\dagger", 1), Op("a", -1))
+                if kk == "J":
+                    new_model[new_e_k] = [e_op + (vv,)]
+                else:
+                    for term in vv:
+                        new_key = new_e_k + kk
+                        new_value = e_op + term
+                        new_model[new_key].append(new_value)
+    return new_model
diff --git a/renormalizer/mps/mps.py b/renormalizer/mps/mps.py
@@ -1808,17 +1808,16 @@ def _mu_regularize(s, epsilon=1e-10):
 
 class BraKetPair:
     def __init__(self, bra_mps, ket_mps, mpo=None):
-        # do copy so that clear_memory won't clear previous braket
-        self.bra_mps = bra_mps.copy()
-        self.ket_mps = ket_mps.copy()
+        self.bra_mps = bra_mps
+        self.ket_mps = ket_mps
         self.mpo = mpo
         self.ft = self.calc_ft()
 
     def calc_ft(self):
         if self.mpo is None:
             dot = self.bra_mps.conj().dot(self.ket_mps)
         else:
-            dot = self.bra_mps.conj().expectation(self.mpo, self.ket_mps)
+            dot = self.ket_mps.expectation(self.mpo, self.bra_mps.conj())
         return complex(
             dot * np.conjugate(self.bra_mps.coeff)
             * self.ket_mps.coeff
@@ -1833,7 +1832,6 @@ def __str__(self):
             ft_str = "%g" % self.ft
         return "bra: %s, ket: %s, ft: %s" % (self.bra_mps, self.ket_mps, ft_str)
 
-    # todo: not used?
     def __iter__(self):
         return iter((self.bra_mps, self.ket_mps))
 

diff --git a/renormalizer/tests/parameter_exact.py b/renormalizer/tests/parameter_exact.py
@@ -4,7 +4,7 @@
 from renormalizer.mps import Mpo
 from renormalizer.model import Phonon, Mol, MolList
 from renormalizer.utils import Quantity
-from renormalizer.utils.qutip_utils import get_clist, get_blist, get_hamiltonian, get_gs
+from renormalizer.utils.qutip_utils import get_clist, get_blist, get_holstein_hamiltonian, get_gs
 
 
 OMEGA = 1
@@ -21,6 +21,6 @@
 qutip_blist = get_blist(N_SITES, N_LEVELS)
 
 G = np.sqrt(DISPLACEMENT**2 * OMEGA / 2)
-qutip_h = get_hamiltonian(N_SITES, J, OMEGA, G, qutip_clist, qutip_blist)
+qutip_h = get_holstein_hamiltonian(N_SITES, J, OMEGA, G, qutip_clist, qutip_blist)
 
 qutip_gs = get_gs(N_SITES, N_LEVELS)
diff --git a/renormalizer/transport/__init__.py b/renormalizer/transport/__init__.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
 # Author: Jiajun Ren <jiajunren0522@gmail.com>
 
-from renormalizer.transport.transport import ChargeTransport, InitElectron, EDGE_THRESHOLD
-from renormalizer.transport.autocorr import TransportAutoCorr
+from renormalizer.transport.kubo import TransportKubo
+from renormalizer.transport.dynamics import ChargeDiffusionDynamics, InitElectron, EDGE_THRESHOLD
diff --git a/renormalizer/transport/autocorr.py b/renormalizer/transport/autocorr.py