Merge branch 'develop' into eden_agreement_hamiltonian_changes

Author: ye-luo

docs/hamiltonianobservable.rst

@@ -509,7 +509,7 @@ density (``density``), number density resolved by particle spin
 (``gofr``), static structure factor (``sk``), static structure factor
 (``skall``), energy density (``energydensity``), one body reduced
 density matrix (``dm1b``), :math:`S(k)` based kinetic energy correction
-(``chiesa``), forward walking (``ForwardWalking``), and force
+(``chiesa``), and force
 (``Force``) estimators. Other estimators are not yet covered.
 
 When an ``<estimator/>`` element appears in ``<hamiltonian/>``, it is
@@ -555,8 +555,6 @@ section (e.g., during VMC only).
   +------------------+------------------+-----------------------------------------------------------+
   |                  | Force            | Family of "force" estimators (see :ref:`ccz-force-est`)   |
   +------------------+------------------+-----------------------------------------------------------+
-  |                  | ForwardWalking   | Forward walking values for existing estimators            |
-  +------------------+------------------+-----------------------------------------------------------+
   |                  | orbitalimages    | Create image files for orbitals, then exit                |
   +------------------+------------------+-----------------------------------------------------------+
   |                  | flux             | Checks sampling of kinetic energy                         |
@@ -1920,90 +1918,6 @@ Additional information:
     <sposet type="bspline" name="dm_basis" size="50" spindataset="0"/>
   </sposet_builder>
 
-.. _forward-walking:
-
-Forward-Walking Estimators
---------------------------
-
-Forward walking is a method for sampling the pure fixed-node
-distribution :math:`\langle \Phi_0 | \Phi_0\rangle`. Specifically, one
-multiplies each walker’s DMC mixed estimate for the observable
-:math:`\mathcal{O}`,
-:math:`\frac{\mathcal{O}(\mathbf{R})\Psi_T(\mathbf{R})}{\Psi_T(\mathbf{R})}`,
-by the weighting factor
-:math:`\frac{\Phi_0(\mathbf{R})}{\Psi_T(\mathbf{R})}`. As it turns out,
-this weighting factor for any walker :math:`\mathbf{R}` is proportional
-to the total number of descendants the walker will have after a
-sufficiently long projection time :math:`\beta`.
-
-To forward walk on an observable, declare a generic forward-walking
-estimator within a ``<hamiltonian>`` block, and then specify the
-observables to forward walk on and the forward-walking parameters. Here
-is a summary.
-
-``estimator type=ForwardWalking`` element:
-
-  +------------------+----------------------+
-  | parent elements: | ``hamiltonian, qmc`` |
-  +------------------+----------------------+
-  | child elements:  | ``Observable``       |
-  +------------------+----------------------+
-
-  attributes:
-
-    +---------------------+--------------+--------------------+-------------+---------------------------+
-    | **Name**            | **Datatype** | **Values**         | **Default** | **Description**           |
-    +=====================+==============+====================+=============+===========================+
-    | ``type``:math:`^r`  | text         | **ForwardWalking** |             | Must be "ForwardWalking"  |
-    +---------------------+--------------+--------------------+-------------+---------------------------+
-    | ``name``:math:`^r`  | text         | *anything*         | any         | Unique name for estimator |
-    +---------------------+--------------+--------------------+-------------+---------------------------+
-
-``Observable`` element:
-
-  +------------------+---------------------------------+
-  | parent elements: | ``estimator, hamiltonian, qmc`` |
-  +------------------+---------------------------------+
-  | child elements:  | *None*                          |
-  +------------------+---------------------------------+
-
-    +--------------------------+--------------+---------------+-------------+---------------------------------------------------------------------------------+
-    | **Name**                 | **Datatype** | **Values**    | **Default** | **Description**                                                                 |
-    +==========================+==============+===============+=============+=================================================================================+
-    | ``name``:math:`^r`       | text         | *anything*    | any         | Registered name of existing estimator on which to forward walk                  |
-    +--------------------------+--------------+---------------+-------------+---------------------------------------------------------------------------------+
-    | ``max``:math:`^r`        | integer      | :math:`>0`    |             | Maximum projection time in steps (``max``:math:`=\beta/\tau`)                   |
-    +--------------------------+--------------+---------------+-------------+---------------------------------------------------------------------------------+
-    | ``frequency``:math:`^r`  | text         | :math:`\geq 1`|             | Dump data only for every ``frequency``-th to ``scalar.dat`` file                |
-    +--------------------------+--------------+---------------+-------------+---------------------------------------------------------------------------------+
-
-Additional information:
-
--  **Cost**: Because histories of observables up to ``max`` time steps
-   have to be stored, the memory cost of storing the nonforward-walked
-   observables variables should be multiplied by :math:`\texttt{max}`.
-   Although this is not an issue for items such as potential energy, it
-   could be prohibitive for observables such as density, forces, etc.
-
--  **Naming Convention**: Forward-walked observables are automatically
-   named ``FWE_name_i``, where ``i`` is the forward-walked expectation
-   value at time step ``i``, and ``name`` is whatever name appears in
-   the ``<Observable>`` block. This is also how it will appear in the
-   ``scalar.dat`` file.
-
-In the following example case, QMCPACK forward walks on the potential
-energy for 300 time steps and dumps the forward-walked value at every
-time step.
-
-.. code-block::
-  :caption: Forward-walking estimator element.
-  :name: Listing 42
-
-  <estimator name="fw" type="ForwardWalking">
-      <Observable name="LocalPotential" max="300" frequency="1"/>
-       <!--- Additional Observable blocks go here -->
-   </estimator>
-
 .. _ccz-force-est:
 
 Chiesa-Ceperley-Zhang Force Estimators

docs/lab_qmc_basics.rst

@@ -1356,7 +1356,7 @@ Container types: ``tuple, list, array, dict, obj``
 ::
 
   from numpy import array  # get array from numpy module
-  from generic import obj  # get obj from Nexus' generic module
+  from developer import obj  # get obj from Nexus' developer module
 
   t=('A',42,56,123.0)     # tuple
 
@@ -1461,7 +1461,7 @@ Iteration: ``for``
 
 ::
 
-  from generic import obj
+  from developer import obj
 
   l = [1,2,3]
   m = [4,5,6]

labs/lab2_qmc_basics/oxygen_atom/ip_conv.py

@@ -4,13 +4,12 @@
 import sys
 from subprocess import Popen,PIPE
 from numpy import array,sqrt,polyfit,polyval,linspace
-from generic import obj
-from plotting import *
+from developer import obj
+import matplotlib.pyplot as plt
 
 params = {'legend.fontsize':14,'figure.facecolor':'white','figure.subplot.hspace':0.6,
-          'axes.labelsize':16,'xtick.labelsize':14,'ytick.labelsize':14}
-rcParams.update(params)
-
+        'axes.labelsize':16,'xtick.labelsize':14,'ytick.labelsize':14}
+plt.rcParams.update(params)
 
 #files = sys.argv[1:]
 
@@ -119,29 +118,29 @@
     print()
     print()
 
-    figure()
-    errorbar(q0.timesteps,q0.energies,q0.errs,fmt='b.',label='q0')
-    plot(tfit,q0fit,'k--',lw=2)
-    title('Oxygen q=0 total energy vs. timestep')
-    ylabel('Total energy (eV)')
-    xlabel('timestep (1/Ha)')
-    legend()
-
-    figure()
-    errorbar(q1.timesteps,q1.energies,q1.errs,fmt='b.',label='q1')
-    plot(tfit,q1fit,'k--',lw=2)
-    title('Oxygen q=1 total energy vs. timestep')
-    ylabel('Total energy (eV)')
-    xlabel('timestep (1/Ha)')
-    legend()
-
-    figure()
-    errorbar(ts,ip,iperr,fmt='r.',label='1st IP')
-    plot(tfit,ipfit,'g--',lw=2)
-    title('Oxygen 1st IP vs. timestep')
-    ylabel('IP (eV)')
-    xlabel('timestep (1/Ha)')
-    legend()
-
-    show()
+    plt.figure()
+    plt.errorbar(q0.timesteps,q0.energies,q0.errs,fmt='b.',label='q0')
+    plt.plot(tfit,q0fit,'k--',lw=2)
+    plt.title('Oxygen q=0 total energy vs. timestep')
+    plt.ylabel('Total energy (eV)')
+    plt.xlabel('timestep (1/Ha)')
+    plt.legend()
+
+    plt.figure()
+    plt.errorbar(q1.timesteps,q1.energies,q1.errs,fmt='b.',label='q1')
+    plt.plot(tfit,q1fit,'k--',lw=2)
+    plt.title('Oxygen q=1 total energy vs. timestep')
+    plt.ylabel('Total energy (eV)')
+    plt.xlabel('timestep (1/Ha)')
+    plt.legend()
+
+    plt.figure()
+    plt.errorbar(ts,ip,iperr,fmt='r.',label='1st IP')
+    plt.plot(tfit,ipfit,'g--',lw=2)
+    plt.title('Oxygen 1st IP vs. timestep')
+    plt.ylabel('IP (eV)')
+    plt.xlabel('timestep (1/Ha)')
+    plt.legend()
+
+    plt.show()
 #end if

labs/lab2_qmc_basics/oxygen_atom/reference/ip_conv.py

@@ -4,12 +4,12 @@
 import sys
 from subprocess import Popen,PIPE
 from numpy import array,sqrt,polyfit,polyval,linspace
-from generic import obj
-from plotting import *
+from developer import obj
+import matplotlib.pyplot as plt
 
 params = {'legend.fontsize':14,'figure.facecolor':'white','figure.subplot.hspace':0.6,
           'axes.labelsize':16,'xtick.labelsize':14,'ytick.labelsize':14}
-rcParams.update(params)
+plt.rcParams.update(params)
 
 
 #files = sys.argv[1:]
@@ -20,7 +20,7 @@
 res = obj()
 for file in files:
     if not os.path.exists(file):
-        print 'file '+file+' does not exist'
+        print('file '+file+' does not exist')
         exit()
     #end if
     prefix    = None
@@ -89,59 +89,59 @@
     ipfit = polyval(polyfit(ts,ip,1),tfit)
 
 
-    print
-    print
-    print 'Total energy (q=0, eV)'
+    print()
+    print()
+    print('Total energy (q=0, eV)')
     for i in range(len(ts)):
-        print '  {0:<6.4f}  {1:<6.4f} +/- {2:<6.4f}'.format(ts[i],q0.energies[i],q0.errs[i])
+        print('  {0:<6.4f}  {1:<6.4f} +/- {2:<6.4f}'.format(ts[i],q0.energies[i],q0.errs[i]))
     #end for
-    print '----------------------------------'
-    print '  {0:<6.4f}  {1:<6.4f}'.format(0.00,q0fit[0])
+    print('----------------------------------')
+    print('  {0:<6.4f}  {1:<6.4f}'.format(0.00,q0fit[0]))
 
-    print
-    print
-    print 'Total energy (q=1, eV)'
+    print()
+    print()
+    print('Total energy (q=1, eV)')
     for i in range(len(ts)):
-        print '  {0:<6.4f}  {1:<6.4f} +/- {2:<6.4f}'.format(ts[i],q1.energies[i],q1.errs[i])
+        print('  {0:<6.4f}  {1:<6.4f} +/- {2:<6.4f}'.format(ts[i],q1.energies[i],q1.errs[i]))
     #end for
-    print '----------------------------------'
-    print '  {0:<6.4f}  {1:<6.4f}'.format(0.00,q1fit[0])
+    print('----------------------------------')
+    print('  {0:<6.4f}  {1:<6.4f}'.format(0.00,q1fit[0]))
 
-    print
-    print
-    print '1st ionization potential (eV)'
+    print()
+    print()
+    print('1st ionization potential (eV)')
     for i in range(len(ts)):
-        print '  {0:<6.4f}  {1:<6.4f} +/- {2:<6.4f}'.format(ts[i],ip[i],iperr[i])
+        print('  {0:<6.4f}  {1:<6.4f} +/- {2:<6.4f}'.format(ts[i],ip[i],iperr[i]))
     #end for
-    print '----------------------------------'
-    print '  {0:<6.4f}  {1:<6.4f}'.format(0.00,ipfit[0])
+    print('----------------------------------')
+    print('  {0:<6.4f}  {1:<6.4f}'.format(0.00,ipfit[0]))
 
-    print
-    print
-
-    figure()
-    errorbar(q0.timesteps,q0.energies,q0.errs,fmt='b.',label='q0')
-    plot(tfit,q0fit,'k--',lw=2)
-    title('Oxygen q=0 total energy vs. timestep')
-    ylabel('Total energy (eV)')
-    xlabel('timestep (1/Ha)')
-    legend()
-
-    figure()
-    errorbar(q1.timesteps,q1.energies,q1.errs,fmt='b.',label='q1')
-    plot(tfit,q1fit,'k--',lw=2)
-    title('Oxygen q=1 total energy vs. timestep')
-    ylabel('Total energy (eV)')
-    xlabel('timestep (1/Ha)')
-    legend()
-
-    figure()
-    errorbar(ts,ip,iperr,fmt='r.',label='1st IP')
-    plot(tfit,ipfit,'g--',lw=2)
-    title('Oxygen 1st IP vs. timestep')
-    ylabel('IP (eV)')
-    xlabel('timestep (1/Ha)')
-    legend()
-
-    show()
+    print()
+    print()
+
+    plt.figure()
+    plt.errorbar(q0.timesteps,q0.energies,q0.errs,fmt='b.',label='q0')
+    plt.plot(tfit,q0fit,'k--',lw=2)
+    plt.title('Oxygen q=0 total energy vs. timestep')
+    plt.ylabel('Total energy (eV)')
+    plt.xlabel('timestep (1/Ha)')
+    plt.legend()
+
+    plt.figure()
+    plt.errorbar(q1.timesteps,q1.energies,q1.errs,fmt='b.',label='q1')
+    plt.plot(tfit,q1fit,'k--',lw=2)
+    plt.title('Oxygen q=1 total energy vs. timestep')
+    plt.ylabel('Total energy (eV)')
+    plt.xlabel('timestep (1/Ha)')
+    plt.legend()
+
+    plt.figure()
+    plt.errorbar(ts,ip,iperr,fmt='r.',label='1st IP')
+    plt.plot(tfit,ipfit,'g--',lw=2)
+    plt.title('Oxygen 1st IP vs. timestep')
+    plt.ylabel('IP (eV)')
+    plt.xlabel('timestep (1/Ha)')
+    plt.legend()
+
+    plt.show()
 #end if

labs/lab2_qmc_basics/oxygen_dimer/dimer_fit.py

@@ -5,8 +5,7 @@
 from numpy import array,polyfit,polyval,linspace,sqrt
 from qmcpack_analyzer import QmcpackAnalyzer
 from unit_converter import convert
-from plotting import *
-from debug import *
+import matplotlib.pyplot as plt
 
 
 args = sys.argv[1:]
@@ -88,12 +87,12 @@
 print('Exp bond length, binding energy:',se,ee)
 
 
-figure()
-errorbar(seps,energies,errors,fmt='r.')
-plot(sf,ef,'g-',lw=2,label='n={0} fit'.format(nfit))
-xlabel('bond length (A)')
-ylabel(Elabel+' (eV)')
-title('DMC '+Elabel+' vs. bond length')
-legend()
+plt.figure()
+plt.errorbar(seps,energies,errors,fmt='r.')
+plt.plot(sf,ef,'g-',lw=2,label='n={0} fit'.format(nfit))
+plt.xlabel('bond length (A)')
+plt.ylabel(Elabel+' (eV)')
+plt.title('DMC '+Elabel+' vs. bond length')
+plt.legend()
 
-show()
+plt.show()