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https://github.com/LCPQ/quantum_package
synced 2024-09-27 03:51:01 +02:00
auto_generate providers in doc
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@ -64,6 +64,7 @@
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.. |MRPT| replace:: :abbr:`MRPT (Multi-Reference Perturbation Theory)`
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.. |PT2| replace:: :abbr:`PT2 (Second order perturbative correction)`
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.. |QMC| replace:: :abbr:`QMC (Quantum Monte Carlo)`
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.. |rst| replace:: :abbr:`RST (ReStructured Text)`
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.. |SCF| replace:: :abbr:`SCF (Self Consistent Field)`
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.. |CASSCF| replace:: |CAS| - |SCF|
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.. |FCIQMC| replace:: |FCI| - |QMC|
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@ -74,3 +75,6 @@
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.. |S^2| replace:: :math:`\widehat{S^2}`
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.. |true| replace:: ``true``
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.. |false| replace:: ``false``
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.. |README| replace:: :file:`README.rst`
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.. |NEED| replace:: :file:`NEED`
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@ -5,7 +5,7 @@ import os
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import ConfigParser
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def generate(abs_module):
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def generate_modules(abs_module, entities):
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MODULE = os.path.split(abs_module)[-1]
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module = MODULE.lower()
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if module == "dummy":
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@ -36,12 +36,112 @@ def generate(abs_module):
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default = ""
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rst += [ ".. option:: %s\n"%(section), doc, default ]
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providers = []
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subroutines = []
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for k in entities:
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e = entities[k]
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if e["module"] == module:
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if "/" not in e["file"] and e["file"] != "ezfio_interface.irp.f":
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if e["type"] == 's':
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subroutines.append(e)
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elif e["type"] == 'p':
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providers.append(e)
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if providers:
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rst += [ "", "Providers", "---------", "" ]
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for p in providers:
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rst += [ """
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.. option:: %s
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.. code:: text
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%s
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File: %s
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%s
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""" % ( p["name"],
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"\n ".join(p["decl"]),
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p["file"],
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" ".join(p["doc"]).replace(".br","\n"),
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) ]
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rst_file = os.path.join('modules',module+".rst")
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with open(rst_file,'w') as f:
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f.write("\n".join(rst))
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def generate_providers(abs_module):
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MODULE = os.path.split(abs_module)[-1]
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module = MODULE.lower()
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if module == "dummy":
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return
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files = {}
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entities = {}
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mandir = os.path.join(abs_module,'IRPF90_man')
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if not os.path.exists(mandir):
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return {}
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for f in os.listdir(mandir):
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filename = os.path.join(mandir,f)
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if f not in files:
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files[f] = 0
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name = f.split('.')[0]
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with open(filename, 'r') as f:
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state = 0
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entity = { "decl": [], "doc": [] ,
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"name": name , "module": module }
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for line in f.readlines():
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line = line.strip()
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if line.startswith(".SH Declaration"):
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state = 1
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continue
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elif line.startswith(".nf"): continue
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elif line.startswith(".ni"): continue
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elif line.startswith(".P"): continue
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if line.startswith(".SH Description"):
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state = 2
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continue
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elif line.startswith(".SH File"):
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state = 3
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continue
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if line.startswith(".SH Need"):
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break
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if line.startswith(".SH Instability"):
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break
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if line.startswith(".SH Call"):
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break
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if state == 1:
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entity["decl"] += [ line ]
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if line.startswith("subroutine") \
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or line.startswith("function ") \
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or " function " in line:
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entity["type"] = 's'
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else:
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entity["type"] = 'p'
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elif state == 2:
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entity["doc"] += [ line ]
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elif state == 3:
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if line.startswith(".br"):
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continue
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entity["file"] = line
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entities [ entity["name"] ] = entity
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return entities
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def main():
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if "QP_ROOT" in os.environ:
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@ -51,11 +151,15 @@ def main():
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SRC = os.path.join(QP_ROOT, "src")
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entities = {}
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for abs_module in os.listdir(SRC):
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abs_module = os.path.join(SRC,abs_module)
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if os.path.exists( os.path.join(abs_module, "README.rst") ):
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generate(abs_module)
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read_entities = generate_providers(abs_module)
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if read_entities:
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for k in read_entities:
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entities[k] = read_entities[k]
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generate_modules(abs_module,entities)
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if __name__ == '__main__':
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main()
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0
docs/source/modules/.gitignore
vendored
Normal file
0
docs/source/modules/.gitignore
vendored
Normal file
@ -47,7 +47,7 @@ zeroth-order Hamiltonian:
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E_{\text{PT2}} = \sum_{ \alpha }
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\frac{|\langle \Psi_S | \hat{H} | \alpha \rangle|^2}
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{E - |\langle \alpha | \hat{H} | \alpha \rangle}
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{E - \langle \alpha | \hat{H} | \alpha \rangle}
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where the |kalpha| determinants are generated by applying all the single and
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double excitation operators to all the determinants of the wave function
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@ -131,3 +131,241 @@ EZFIO parameters
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Calculated |FCI| energy + |PT2|
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Providers
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---------
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.. option:: pt2_e0_denominator
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.. code:: text
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double precision, allocatable :: pt2_e0_denominator (N_states)
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File: energy.irp.f
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E0 in the denominator of the PT2
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.. option:: pt2_u_0
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.. code:: text
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double precision, allocatable :: pt2_w (N_det_generators)
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double precision, allocatable :: pt2_cw (0:N_det_generators)
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double precision :: pt2_w_t
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double precision :: pt2_u_0
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integer, allocatable :: pt2_n_0 (pt2_N_teeth+1)
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_r
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.. code:: text
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integer, allocatable :: pt2_j (N_det_generators)
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integer, allocatable :: pt2_r (N_det_generators)
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_w
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.. code:: text
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double precision, allocatable :: pt2_w (N_det_generators)
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double precision, allocatable :: pt2_cw (0:N_det_generators)
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double precision :: pt2_w_t
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double precision :: pt2_u_0
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integer, allocatable :: pt2_n_0 (pt2_N_teeth+1)
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_u
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.. code:: text
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double precision, allocatable :: pt2_u (N_det_generators)
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_j
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.. code:: text
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integer, allocatable :: pt2_j (N_det_generators)
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integer, allocatable :: pt2_r (N_det_generators)
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_f
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.. code:: text
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integer, allocatable :: pt2_f (N_det_generators)
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integer :: pt2_n_tasks_max
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_cw
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.. code:: text
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double precision, allocatable :: pt2_w (N_det_generators)
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double precision, allocatable :: pt2_cw (0:N_det_generators)
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double precision :: pt2_w_t
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double precision :: pt2_u_0
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integer, allocatable :: pt2_n_0 (pt2_N_teeth+1)
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_w_t
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.. code:: text
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double precision, allocatable :: pt2_w (N_det_generators)
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double precision, allocatable :: pt2_cw (0:N_det_generators)
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double precision :: pt2_w_t
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double precision :: pt2_u_0
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integer, allocatable :: pt2_n_0 (pt2_N_teeth+1)
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_n_tasks
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.. code:: text
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integer :: pt2_n_tasks
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File: pt2_stoch_routines.irp.f
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Number of parallel tasks for the Monte Carlo
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.. option:: pt2_n_0
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.. code:: text
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double precision, allocatable :: pt2_w (N_det_generators)
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double precision, allocatable :: pt2_cw (0:N_det_generators)
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double precision :: pt2_w_t
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double precision :: pt2_u_0
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integer, allocatable :: pt2_n_0 (pt2_N_teeth+1)
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_n_tasks_max
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.. code:: text
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integer, allocatable :: pt2_f (N_det_generators)
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integer :: pt2_n_tasks_max
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_n_teeth
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.. code:: text
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integer :: pt2_n_teeth
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integer :: pt2_mindetinfirstteeth
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File: pt2_stoch_routines.irp.f
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.. option:: initialize_pt2_e0_denominator
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.. code:: text
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logical :: initialize_pt2_e0_denominator
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File: energy.irp.f
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If true, initialize pt2_E0_denominator
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.. option:: pt2_mindetinfirstteeth
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.. code:: text
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integer :: pt2_n_teeth
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integer :: pt2_mindetinfirstteeth
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File: pt2_stoch_routines.irp.f
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.. option:: pt2_stoch_istate
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.. code:: text
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integer :: pt2_stoch_istate
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File: pt2_stoch_routines.irp.f
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State for stochatsic PT2
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@ -95,3 +95,315 @@ EZFIO parameters
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If |true|, skip the (inactive+core) --> (active) and the (active) --> (virtual) orbital rotations within the |SCF| procedure
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Default: False
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Providers
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---------
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.. option:: fock_matrix_mo_alpha
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.. code:: text
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double precision, allocatable :: fock_matrix_mo_alpha (mo_tot_num,mo_tot_num)
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File: Fock_matrix.irp.f
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Fock matrix on the MO basis
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.. option:: extrapolate_fock_matrix
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.. code:: text
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subroutine extrapolate_Fock_matrix( &
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error_matrix_DIIS,Fock_matrix_DIIS, &
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Fock_matrix_AO_,size_Fock_matrix_AO, &
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iteration_SCF,dim_DIIS &
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)
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File: Roothaan_Hall_SCF.irp.f
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Compute the extrapolated Fock matrix using the DIIS procedure
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.. option:: fock_matrix_ao_alpha
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.. code:: text
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double precision, allocatable :: fock_matrix_ao_alpha (ao_num,ao_num)
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double precision, allocatable :: fock_matrix_ao_beta (ao_num,ao_num)
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File: Fock_matrix.irp.f
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Alpha Fock matrix in AO basis set
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.. option:: hf_energy
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.. code:: text
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double precision :: hf_energy
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File: Fock_matrix.irp.f
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Hartree-Fock energy
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.. option:: fock_matrix_diag_mo
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.. code:: text
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double precision, allocatable :: fock_matrix_mo (mo_tot_num,mo_tot_num)
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double precision, allocatable :: fock_matrix_diag_mo (mo_tot_num)
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File: Fock_matrix.irp.f
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Fock matrix on the MO basis. For open shells, the ROHF Fock Matrix is
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| F-K | F + K/2 | F | |---------------------------------| | F + K/2 | F | F - K/2 | |---------------------------------| | F | F - K/2 | F + K |
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F = 1/2 (Fa + Fb)
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K = Fb - Fa
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.. option:: fock_matrix_ao_beta
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.. code:: text
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double precision, allocatable :: fock_matrix_ao_alpha (ao_num,ao_num)
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double precision, allocatable :: fock_matrix_ao_beta (ao_num,ao_num)
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File: Fock_matrix.irp.f
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Alpha Fock matrix in AO basis set
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.. option:: hf_density_matrix_ao
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.. code:: text
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double precision, allocatable :: hf_density_matrix_ao (ao_num,ao_num)
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File: HF_density_matrix_ao.irp.f
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S^{-1}.P.S^{-1} where P = C.C^t
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.. option:: fps_spf_matrix_ao
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.. code:: text
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double precision, allocatable :: fps_spf_matrix_ao (AO_num,AO_num)
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File: DIIS.irp.f
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Commutator FPS - SPF
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.. option:: threshold_diis_nonzero
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.. code:: text
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double precision :: threshold_diis_nonzero
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File: DIIS.irp.f
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If threshold_DIIS is zero, choose sqrt(thresh_scf)
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.. option:: ao_bi_elec_integral_alpha
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.. code:: text
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double precision, allocatable :: ao_bi_elec_integral_alpha (ao_num,ao_num)
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double precision, allocatable :: ao_bi_elec_integral_beta (ao_num,ao_num)
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File: Fock_matrix.irp.f
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Alpha Fock matrix in AO basis set
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.. option:: eigenvectors_fock_matrix_ao
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.. code:: text
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double precision, allocatable :: eigenvalues_fock_matrix_ao (AO_num)
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double precision, allocatable :: eigenvectors_fock_matrix_ao (AO_num,AO_num)
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File: DIIS.irp.f
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Eigenvalues and eigenvectors of the Fock matrix over the AO basis
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.. option:: fock_matrix_mo_beta
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.. code:: text
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double precision, allocatable :: fock_matrix_mo_beta (mo_tot_num,mo_tot_num)
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File: Fock_matrix.irp.f
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Fock matrix on the MO basis
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.. option:: eigenvectors_fock_matrix_mo
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|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: diagonal_fock_matrix_mo (mo_tot_num)
|
||||
double precision, allocatable :: eigenvectors_fock_matrix_mo (ao_num,mo_tot_num)
|
||||
|
||||
File: diagonalize_fock.irp.f
|
||||
|
||||
Diagonal Fock matrix in the MO basis
|
||||
|
||||
|
||||
|
||||
|
||||
.. option:: fock_matrix_mo
|
||||
|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: fock_matrix_mo (mo_tot_num,mo_tot_num)
|
||||
double precision, allocatable :: fock_matrix_diag_mo (mo_tot_num)
|
||||
|
||||
File: Fock_matrix.irp.f
|
||||
|
||||
Fock matrix on the MO basis. For open shells, the ROHF Fock Matrix is
|
||||
| F-K | F + K/2 | F | |---------------------------------| | F + K/2 | F | F - K/2 | |---------------------------------| | F | F - K/2 | F + K |
|
||||
F = 1/2 (Fa + Fb)
|
||||
K = Fb - Fa
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
.. option:: fps_spf_matrix_mo
|
||||
|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: fps_spf_matrix_mo (mo_tot_num,mo_tot_num)
|
||||
|
||||
File: DIIS.irp.f
|
||||
|
||||
Commutator FPS - SPF in MO basis
|
||||
|
||||
|
||||
|
||||
|
||||
.. option:: diagonal_fock_matrix_mo_sum
|
||||
|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: diagonal_fock_matrix_mo_sum (mo_tot_num)
|
||||
|
||||
File: diagonalize_fock.irp.f
|
||||
|
||||
diagonal element of the fock matrix calculated as the sum over all the interactions with all the electrons in the RHF determinant diagonal_Fock_matrix_mo_sum(i) = sum_{j=1, N_elec} 2 J_ij -K_ij
|
||||
|
||||
|
||||
|
||||
|
||||
.. option:: hf_density_matrix_ao_alpha
|
||||
|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: hf_density_matrix_ao_alpha (ao_num,ao_num)
|
||||
|
||||
File: HF_density_matrix_ao.irp.f
|
||||
|
||||
S^{-1}.P_alpha.S^{-1}
|
||||
|
||||
|
||||
|
||||
|
||||
.. option:: hf_density_matrix_ao_beta
|
||||
|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: hf_density_matrix_ao_beta (ao_num,ao_num)
|
||||
|
||||
File: HF_density_matrix_ao.irp.f
|
||||
|
||||
S^{-1}.P_beta.S^{-1}
|
||||
|
||||
|
||||
|
||||
|
||||
.. option:: eigenvalues_fock_matrix_ao
|
||||
|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: eigenvalues_fock_matrix_ao (AO_num)
|
||||
double precision, allocatable :: eigenvectors_fock_matrix_ao (AO_num,AO_num)
|
||||
|
||||
File: DIIS.irp.f
|
||||
|
||||
Eigenvalues and eigenvectors of the Fock matrix over the AO basis
|
||||
|
||||
|
||||
|
||||
|
||||
.. option:: ao_bi_elec_integral_beta
|
||||
|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: ao_bi_elec_integral_alpha (ao_num,ao_num)
|
||||
double precision, allocatable :: ao_bi_elec_integral_beta (ao_num,ao_num)
|
||||
|
||||
File: Fock_matrix.irp.f
|
||||
|
||||
Alpha Fock matrix in AO basis set
|
||||
|
||||
|
||||
|
||||
|
||||
.. option:: fock_matrix_ao
|
||||
|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: fock_matrix_ao (ao_num,ao_num)
|
||||
|
||||
File: Fock_matrix.irp.f
|
||||
|
||||
Fock matrix in AO basis set
|
||||
|
||||
|
||||
|
||||
|
||||
.. option:: diagonal_fock_matrix_mo
|
||||
|
||||
.. code:: text
|
||||
|
||||
double precision, allocatable :: diagonal_fock_matrix_mo (mo_tot_num)
|
||||
double precision, allocatable :: eigenvectors_fock_matrix_mo (ao_num,mo_tot_num)
|
||||
|
||||
File: diagonalize_fock.irp.f
|
||||
|
||||
Diagonal Fock matrix in the MO basis
|
||||
|
||||
|
||||
|
||||
@ -1,7 +1,9 @@
|
||||
================
|
||||
Index of Modules
|
||||
================
|
||||
=====================
|
||||
Index for programmers
|
||||
=====================
|
||||
|
||||
Index of Modules
|
||||
----------------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
@ -10,3 +12,23 @@ Index of Modules
|
||||
/modules/*
|
||||
|
||||
|
||||
Index of Providers
|
||||
------------------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:glob:
|
||||
|
||||
/providers/*
|
||||
|
||||
|
||||
Index of Subroutines/Functions
|
||||
------------------------------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
:glob:
|
||||
|
||||
/subroutines/*
|
||||
|
||||
|
||||
|
||||
@ -1,11 +1,78 @@
|
||||
=======================
|
||||
Programming in the |qp|
|
||||
=======================
|
||||
|
||||
To program in the |qp|, it is required that you are familiar with
|
||||
the `IRPF90`_ code generator. A gitbook can be found
|
||||
`here <http://scemama.gitbooks.io/irpf90>`_.
|
||||
To program in the |qp|, it is required that you are familiar with the |IRPF90|
|
||||
code generator. A GitBook can be found `here <http://scemama.gitbooks.io/irpf90>`_,
|
||||
and programmers are encouraged to visit this manual.
|
||||
|
||||
|IRPF90| make programming very simple. The only information a programmer needs
|
||||
in order to write a new program is the name of the required |IRPF90| entities
|
||||
which may already exist in other modules. For example, writing a program which
|
||||
prints the Hartree-Fock energy is as simple as:
|
||||
|
||||
.. code:: irpf90
|
||||
|
||||
program print_hf_energy
|
||||
implicit none
|
||||
BEGIN_DOC
|
||||
! Program which prints the Hartree-Fock energy
|
||||
! to the standard output
|
||||
END_DOC
|
||||
print *, 'HF energy = ', HF_energy
|
||||
end
|
||||
|
||||
|
||||
The only required information was the existence of a provider for
|
||||
:command:`hf_energy`. A detailed list of all the providers, subroutines
|
||||
and functions of the |qp| can be found in the appendix of this manual.
|
||||
|
||||
|
||||
|
||||
Architecture
|
||||
============
|
||||
|
||||
As |IRPF90| is used, the programmer doesn't have a full control of the sequence
|
||||
of instructions in the produced Fortran code. This explains why the input data
|
||||
is stored in a database rather than in sequential text files. Indeed, the
|
||||
programmer can't know by advance in which order the files will be read, so a
|
||||
simple random access to persistent data is needed. The |EZFIO| library generator
|
||||
is a practical answer to this problem.
|
||||
|
||||
The |qp| uses a collection of programs inter-operating together. Each of these
|
||||
programs is reading and/or modifying information in the |EZFIO| database.
|
||||
This is done mostly using the command line or scripting.
|
||||
|
||||
.. important::
|
||||
|
||||
Each command modifies the state of the |EZFIO| database, so running twice the
|
||||
same program on the same database may have different behaviors because of the
|
||||
state of the database. For reproducibility, users are encouraged to run scripts
|
||||
where a fresg new |EZFIO| database is created at the beginning of the
|
||||
script. This way of running the |qp| makes calculations reproducible.
|
||||
|
||||
|
||||
The computational part |qp| is organized in **modules**. A module is a
|
||||
directory which contains multiple |IRPF90| files, a |README| and a |NEED| file.
|
||||
|
||||
The |README| file contains documentation about the module, that is
|
||||
automatically included in the documentation of the |qp|. The documentation is
|
||||
generated by the `Sphinx documentation builder <http://www.sphinx-doc.org>`_,
|
||||
and it should be written using the |rst| format.
|
||||
|
||||
The |NEED| file contains the list of the modules which are needed for the
|
||||
current module. When a module is needed, it means that all the |IRPF90| files
|
||||
it contains should be included in the current module. This is done
|
||||
automatically during the building process, by creating symbolic links in the
|
||||
current directory.
|
||||
|
||||
To compile the program, the |Ninja| build system is used, and all the building
|
||||
process is fully automated such that the programmer will never have to modify a
|
||||
file by hand. Running :command:`ninja` inside a module will compile only the
|
||||
module, and running :command:`ninja` at the root of the |qp| will build all the
|
||||
modules, as well as the tools.
|
||||
|
||||
.. cache compile
|
||||
.. interface AOs / MOs => resultsFile
|
||||
.. interface integrals => AO / MO
|
||||
.. interface integrals MO => FCIDUMP
|
||||
|
||||
Loading…
Reference in New Issue
Block a user