else:
if self.name!=self.parentname:
logger.info(f'Built {self.name} using topology of {self.parentname}; copying {self.parentname}.top to {self.name}.top')
- self.load_top_gro(f'{self.parentname}.top',f'{self.name}.gro',tpxfilename=f'{self.name}.tpx',wrap_coords=False)
+ self.load_top_gro(f'{self.parentname}.top',f'{self.name}.gro',tpxfilename=f'{self.parentname}.tpx',wrap_coords=False)
shutil.copy(f'{self.parentname}.top',f'{self.name}.top')
shutil.copy(f'{self.parentname}.grx',f'{self.name}.grx')
shutil.copy(f'{self.parentname}.tpx',f'{self.name}.tpx')
diff --git a/_sources/user-guide/program-flow.rst.txt b/_sources/user-guide/program-flow.rst.txt
index 20516d8..e8443d2 100644
--- a/_sources/user-guide/program-flow.rst.txt
+++ b/_sources/user-guide/program-flow.rst.txt
@@ -7,7 +7,7 @@ Program Flow
``htpolynet run`` workflow.
-A basic depiction of the the workflow initiated by ``htpolynet run`` is shown in the figure above. The "0"th step is generation of the molecular structure data for any monomeric reactants, in the form of either Sybyl ``mol2`` or RCSB ``pdb`` files. ``HTPolyNet`` does **not** do this, we provide some general guidance :ref:`here ` and some specific example cases in the :ref:`tutorials `. Then, based on instructions in the :ref:`configuration file `, ``HTPolyNet`` proceeds with setting up all reactions and oligomer templates. Once these are generated, it then generates the full initial system topology in Gromacs format (that is, it generates a ``top`` file), and an initial set of coordinates (a ``gro`` file). Since the initial coordinates are built a low density (typically), ``HTPolyNet`` then performs MD to "densify" the system, followed by any pre-cure equilibration the user would like. Then the :ref:`CURE algorithm ` takes over to generate intermolecular bonds and drive the polymerization. Once it finishes, ``HTPolyNet`` conducts any post-cure equilibration the user likes, before saving the final ``top`` and ``gro`` file. All of this work happens in the project subdirectory of the current directory in which `` run`` is invoked.
+A basic depiction of the the workflow initiated by ``htpolynet run`` is shown in the figure above. The "0"th step is generation of the molecular structure data for any monomeric reactants, in the form of either Sybyl ``mol2`` or RCSB ``pdb`` files. ``HTPolyNet`` does **not** do this; we provide some general guidance :ref:`here ` and some specific example cases in the :ref:`tutorials `. Then, based on instructions in the :ref:`configuration file `, ``HTPolyNet`` proceeds with setting up all reactions and oligomer templates. Once these are generated, it then generates the full initial system topology in Gromacs format (that is, it generates a ``top`` file), and an initial set of coordinates (a ``gro`` file). Since the initial coordinates are built a low density (typically), ``HTPolyNet`` then performs MD to "densify" the system, followed by any pre-cure equilibration the user would like. Then the :ref:`CURE algorithm ` takes over to generate intermolecular bonds and drive the polymerization. Once it finishes, ``HTPolyNet`` conducts any post-cure equilibration the user likes, before saving the final ``top`` and ``gro`` file. All of this work happens in the project subdirectory of the current directory in which ``run`` is invoked.
This workflow should make clear that the two required tasks of the user are:
@@ -25,7 +25,7 @@ The Connect-Update-Relax-Equilibrate (CURE) algorithm
Block flow diagram of the CURE algorithm used in ``HTPolyNet``.
-The algorithm used to create new bonds and polymerize a system is called the CURE algorithm, depicted above. This is just a slightly modified version of a standard search-radius-type algorithm, first used by Li and Strahan to study EPON/DETDA thermosets :cite:t:`Li2010Crosslinking`. The CURE algorithm begins by executing a search for new bonds on a frozen system configuration. Bonds are downselected through a series of filters to arrive at a final set of bonds to form. If the distance between any pair of "bond-designate" atoms is greater than some threshold (the ``trigger_distance`` parameter in the :ref:`drag subdirective ` of the ``CURE`` directive of a configuration file), a series of MD simulations that slowly bring all to-be-bound atom closer together is performed. Then the topology is updated, where ``HTPolyNet`` applies the charges, atom type, and bonded interaction templates from the oligomer template set to each bond. After the update, a series of relaxation MD simulations bring all bonds to their equilibrium lengths. Then a short NPT MD simulation equilibrates the overall density before initiating the next CURE iteration. CURE iterations continue until (a) a desired conversion is reached, or (b) no new allowable bonds are identified.
+The algorithm used to create new bonds and polymerize a system is called the CURE algorithm, depicted above. This is just a slightly modified version of a standard search-radius-type algorithm, first used by Li and Strahan to study EPON/DETDA thermosets (:cite:t:`Li2010Crosslinking`). The CURE algorithm begins by executing a search for new bonds on a frozen system configuration. Bonds are downselected through a series of filters to arrive at a final set of bonds to form. If the distance between any pair of "bond-designate" atoms is greater than some threshold (the ``trigger_distance`` parameter in the :ref:`drag subdirective ` of the ``CURE`` directive of a configuration file), a series of MD simulations that slowly bring all to-be-bound atom closer together is performed. Then the topology is updated, where ``HTPolyNet`` applies the charges, atom type, and bonded interaction templates from the oligomer template set to each bond. After the update, a series of relaxation MD simulations bring all bonds to their equilibrium lengths. Then a short NPT MD simulation equilibrates the overall density before initiating the next CURE iteration. CURE iterations continue until (a) a desired conversion is reached, or (b) no new allowable bonds are identified.
.. _bondsearch_filters:
diff --git a/user-guide/program-flow.html b/user-guide/program-flow.html
index bb097a1..7286859 100644
--- a/user-guide/program-flow.html
+++ b/user-guide/program-flow.html
@@ -39,7 +39,7 @@ Program FlowFig. 3 htpolynet run workflow.¶
-
A basic depiction of the the workflow initiated by htpolynet run is shown in the figure above. The “0”th step is generation of the molecular structure data for any monomeric reactants, in the form of either Sybyl mol2 or RCSB pdb files. HTPolyNet does not do this, we provide some general guidance here and some specific example cases in the tutorials. Then, based on instructions in the configuration file, HTPolyNet proceeds with setting up all reactions and oligomer templates. Once these are generated, it then generates the full initial system topology in Gromacs format (that is, it generates a top file), and an initial set of coordinates (a gro file). Since the initial coordinates are built a low density (typically), HTPolyNet then performs MD to “densify” the system, followed by any pre-cure equilibration the user would like. Then the CURE algorithm takes over to generate intermolecular bonds and drive the polymerization. Once it finishes, HTPolyNet conducts any post-cure equilibration the user likes, before saving the final top and gro file. All of this work happens in the project subdirectory of the current directory in which `` run`` is invoked.
+A basic depiction of the the workflow initiated by htpolynet run is shown in the figure above. The “0”th step is generation of the molecular structure data for any monomeric reactants, in the form of either Sybyl mol2 or RCSB pdb files. HTPolyNet does not do this; we provide some general guidance here and some specific example cases in the tutorials. Then, based on instructions in the configuration file, HTPolyNet proceeds with setting up all reactions and oligomer templates. Once these are generated, it then generates the full initial system topology in Gromacs format (that is, it generates a top file), and an initial set of coordinates (a gro file). Since the initial coordinates are built a low density (typically), HTPolyNet then performs MD to “densify” the system, followed by any pre-cure equilibration the user would like. Then the CURE algorithm takes over to generate intermolecular bonds and drive the polymerization. Once it finishes, HTPolyNet conducts any post-cure equilibration the user likes, before saving the final top and gro file. All of this work happens in the project subdirectory of the current directory in which run is invoked.
This workflow should make clear that the two required tasks of the user are:
Program FlowFig. 4 Block flow diagram of the CURE algorithm used in HTPolyNet.¶
-
The algorithm used to create new bonds and polymerize a system is called the CURE algorithm, depicted above. This is just a slightly modified version of a standard search-radius-type algorithm, first used by Li and Strahan to study EPON/DETDA thermosets Li and Strachan [LS10]. The CURE algorithm begins by executing a search for new bonds on a frozen system configuration. Bonds are downselected through a series of filters to arrive at a final set of bonds to form. If the distance between any pair of “bond-designate” atoms is greater than some threshold (the trigger_distance parameter in the drag subdirective of the CURE directive of a configuration file), a series of MD simulations that slowly bring all to-be-bound atom closer together is performed. Then the topology is updated, where HTPolyNet applies the charges, atom type, and bonded interaction templates from the oligomer template set to each bond. After the update, a series of relaxation MD simulations bring all bonds to their equilibrium lengths. Then a short NPT MD simulation equilibrates the overall density before initiating the next CURE iteration. CURE iterations continue until (a) a desired conversion is reached, or (b) no new allowable bonds are identified.
+The algorithm used to create new bonds and polymerize a system is called the CURE algorithm, depicted above. This is just a slightly modified version of a standard search-radius-type algorithm, first used by Li and Strahan to study EPON/DETDA thermosets (Li and Strachan [LS10]). The CURE algorithm begins by executing a search for new bonds on a frozen system configuration. Bonds are downselected through a series of filters to arrive at a final set of bonds to form. If the distance between any pair of “bond-designate” atoms is greater than some threshold (the trigger_distance parameter in the drag subdirective of the CURE directive of a configuration file), a series of MD simulations that slowly bring all to-be-bound atom closer together is performed. Then the topology is updated, where HTPolyNet applies the charges, atom type, and bonded interaction templates from the oligomer template set to each bond. After the update, a series of relaxation MD simulations bring all bonds to their equilibrium lengths. Then a short NPT MD simulation equilibrates the overall density before initiating the next CURE iteration. CURE iterations continue until (a) a desired conversion is reached, or (b) no new allowable bonds are identified.
Identifying allowable bonds: Bondsearch filters¶