--- /dev/null
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+Licenses are intended to guarantee your freedom to share and change
+free software--to make sure the software is free for all its users.
+
+ This license, the Lesser General Public License, applies to some
+specially designated software packages--typically libraries--of the
+Free Software Foundation and other authors who decide to use it. You
+can use it too, but we suggest you first think carefully about whether
+this license or the ordinary General Public License is the better
+strategy to use in any particular case, based on the explanations below.
+
+ When we speak of free software, we are referring to freedom of use,
+not price. Our General Public Licenses are designed to make sure that
+you have the freedom to distribute copies of free software (and charge
+for this service if you wish); that you receive source code or can get
+it if you want it; that you can change the software and use pieces of
+it in new free programs; and that you are informed that you can do
+these things.
+
+ To protect your rights, we need to make restrictions that forbid
+distributors to deny you these rights or to ask you to surrender these
+rights. These restrictions translate to certain responsibilities for
+you if you distribute copies of the library or if you modify it.
+
+ For example, if you distribute copies of the library, whether gratis
+or for a fee, you must give the recipients all the rights that we gave
+you. You must make sure that they, too, receive or can get the source
+code. If you link other code with the library, you must provide
+complete object files to the recipients, so that they can relink them
+with the library after making changes to the library and recompiling
+it. And you must show them these terms so they know their rights.
+
+ We protect your rights with a two-step method: (1) we copyright the
+library, and (2) we offer you this license, which gives you legal
+permission to copy, distribute and/or modify the library.
+
+ To protect each distributor, we want to make it very clear that
+there is no warranty for the free library. Also, if the library is
+modified by someone else and passed on, the recipients should know
+that what they have is not the original version, so that the original
+author's reputation will not be affected by problems that might be
+introduced by others.
+\f
+ Finally, software patents pose a constant threat to the existence of
+any free program. We wish to make sure that a company cannot
+effectively restrict the users of a free program by obtaining a
+restrictive license from a patent holder. Therefore, we insist that
+any patent license obtained for a version of the library must be
+consistent with the full freedom of use specified in this license.
+
+ Most GNU software, including some libraries, is covered by the
+ordinary GNU General Public License. This license, the GNU Lesser
+General Public License, applies to certain designated libraries, and
+is quite different from the ordinary General Public License. We use
+this license for certain libraries in order to permit linking those
+libraries into non-free programs.
+
+ When a program is linked with a library, whether statically or using
+a shared library, the combination of the two is legally speaking a
+combined work, a derivative of the original library. The ordinary
+General Public License therefore permits such linking only if the
+entire combination fits its criteria of freedom. The Lesser General
+Public License permits more lax criteria for linking other code with
+the library.
+
+ We call this license the "Lesser" General Public License because it
+does Less to protect the user's freedom than the ordinary General
+Public License. It also provides other free software developers Less
+of an advantage over competing non-free programs. These disadvantages
+are the reason we use the ordinary General Public License for many
+libraries. However, the Lesser license provides advantages in certain
+special circumstances.
+
+ For example, on rare occasions, there may be a special need to
+encourage the widest possible use of a certain library, so that it becomes
+a de-facto standard. To achieve this, non-free programs must be
+allowed to use the library. A more frequent case is that a free
+library does the same job as widely used non-free libraries. In this
+case, there is little to gain by limiting the free library to free
+software only, so we use the Lesser General Public License.
+
+ In other cases, permission to use a particular library in non-free
+programs enables a greater number of people to use a large body of
+free software. For example, permission to use the GNU C Library in
+non-free programs enables many more people to use the whole GNU
+operating system, as well as its variant, the GNU/Linux operating
+system.
+
+ Although the Lesser General Public License is Less protective of the
+users' freedom, it does ensure that the user of a program that is
+linked with the Library has the freedom and the wherewithal to run
+that program using a modified version of the Library.
+
+ The precise terms and conditions for copying, distribution and
+modification follow. Pay close attention to the difference between a
+"work based on the library" and a "work that uses the library". The
+former contains code derived from the library, whereas the latter must
+be combined with the library in order to run.
+\f
+ GNU LESSER GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License Agreement applies to any software library or other
+program which contains a notice placed by the copyright holder or
+other authorized party saying it may be distributed under the terms of
+this Lesser General Public License (also called "this License").
+Each licensee is addressed as "you".
+
+ A "library" means a collection of software functions and/or data
+prepared so as to be conveniently linked with application programs
+(which use some of those functions and data) to form executables.
+
+ The "Library", below, refers to any such software library or work
+which has been distributed under these terms. A "work based on the
+Library" means either the Library or any derivative work under
+copyright law: that is to say, a work containing the Library or a
+portion of it, either verbatim or with modifications and/or translated
+straightforwardly into another language. (Hereinafter, translation is
+included without limitation in the term "modification".)
+
+ "Source code" for a work means the preferred form of the work for
+making modifications to it. For a library, complete source code means
+all the source code for all modules it contains, plus any associated
+interface definition files, plus the scripts used to control compilation
+and installation of the library.
+
+ Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of
+running a program using the Library is not restricted, and output from
+such a program is covered only if its contents constitute a work based
+on the Library (independent of the use of the Library in a tool for
+writing it). Whether that is true depends on what the Library does
+and what the program that uses the Library does.
+
+ 1. You may copy and distribute verbatim copies of the Library's
+complete source code as you receive it, in any medium, provided that
+you conspicuously and appropriately publish on each copy an
+appropriate copyright notice and disclaimer of warranty; keep intact
+all the notices that refer to this License and to the absence of any
+warranty; and distribute a copy of this License along with the
+Library.
+
+ You may charge a fee for the physical act of transferring a copy,
+and you may at your option offer warranty protection in exchange for a
+fee.
+\f
+ 2. You may modify your copy or copies of the Library or any portion
+of it, thus forming a work based on the Library, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+ a) The modified work must itself be a software library.
+
+ b) You must cause the files modified to carry prominent notices
+ stating that you changed the files and the date of any change.
+
+ c) You must cause the whole of the work to be licensed at no
+ charge to all third parties under the terms of this License.
+
+ d) If a facility in the modified Library refers to a function or a
+ table of data to be supplied by an application program that uses
+ the facility, other than as an argument passed when the facility
+ is invoked, then you must make a good faith effort to ensure that,
+ in the event an application does not supply such function or
+ table, the facility still operates, and performs whatever part of
+ its purpose remains meaningful.
+
+ (For example, a function in a library to compute square roots has
+ a purpose that is entirely well-defined independent of the
+ application. Therefore, Subsection 2d requires that any
+ application-supplied function or table used by this function must
+ be optional: if the application does not supply it, the square
+ root function must still compute square roots.)
+
+These requirements apply to the modified work as a whole. If
+identifiable sections of that work are not derived from the Library,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works. But when you
+distribute the same sections as part of a whole which is a work based
+on the Library, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote
+it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Library.
+
+In addition, mere aggregation of another work not based on the Library
+with the Library (or with a work based on the Library) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+ 3. You may opt to apply the terms of the ordinary GNU General Public
+License instead of this License to a given copy of the Library. To do
+this, you must alter all the notices that refer to this License, so
+that they refer to the ordinary GNU General Public License, version 2,
+instead of to this License. (If a newer version than version 2 of the
+ordinary GNU General Public License has appeared, then you can specify
+that version instead if you wish.) Do not make any other change in
+these notices.
+\f
+ Once this change is made in a given copy, it is irreversible for
+that copy, so the ordinary GNU General Public License applies to all
+subsequent copies and derivative works made from that copy.
+
+ This option is useful when you wish to copy part of the code of
+the Library into a program that is not a library.
+
+ 4. You may copy and distribute the Library (or a portion or
+derivative of it, under Section 2) in object code or executable form
+under the terms of Sections 1 and 2 above provided that you accompany
+it with the complete corresponding machine-readable source code, which
+must be distributed under the terms of Sections 1 and 2 above on a
+medium customarily used for software interchange.
+
+ If distribution of object code is made by offering access to copy
+from a designated place, then offering equivalent access to copy the
+source code from the same place satisfies the requirement to
+distribute the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+ 5. A program that contains no derivative of any portion of the
+Library, but is designed to work with the Library by being compiled or
+linked with it, is called a "work that uses the Library". Such a
+work, in isolation, is not a derivative work of the Library, and
+therefore falls outside the scope of this License.
+
+ However, linking a "work that uses the Library" with the Library
+creates an executable that is a derivative of the Library (because it
+contains portions of the Library), rather than a "work that uses the
+library". The executable is therefore covered by this License.
+Section 6 states terms for distribution of such executables.
+
+ When a "work that uses the Library" uses material from a header file
+that is part of the Library, the object code for the work may be a
+derivative work of the Library even though the source code is not.
+Whether this is true is especially significant if the work can be
+linked without the Library, or if the work is itself a library. The
+threshold for this to be true is not precisely defined by law.
+
+ If such an object file uses only numerical parameters, data
+structure layouts and accessors, and small macros and small inline
+functions (ten lines or less in length), then the use of the object
+file is unrestricted, regardless of whether it is legally a derivative
+work. (Executables containing this object code plus portions of the
+Library will still fall under Section 6.)
+
+ Otherwise, if the work is a derivative of the Library, you may
+distribute the object code for the work under the terms of Section 6.
+Any executables containing that work also fall under Section 6,
+whether or not they are linked directly with the Library itself.
+\f
+ 6. As an exception to the Sections above, you may also combine or
+link a "work that uses the Library" with the Library to produce a
+work containing portions of the Library, and distribute that work
+under terms of your choice, provided that the terms permit
+modification of the work for the customer's own use and reverse
+engineering for debugging such modifications.
+
+ You must give prominent notice with each copy of the work that the
+Library is used in it and that the Library and its use are covered by
+this License. You must supply a copy of this License. If the work
+during execution displays copyright notices, you must include the
+copyright notice for the Library among them, as well as a reference
+directing the user to the copy of this License. Also, you must do one
+of these things:
+
+ a) Accompany the work with the complete corresponding
+ machine-readable source code for the Library including whatever
+ changes were used in the work (which must be distributed under
+ Sections 1 and 2 above); and, if the work is an executable linked
+ with the Library, with the complete machine-readable "work that
+ uses the Library", as object code and/or source code, so that the
+ user can modify the Library and then relink to produce a modified
+ executable containing the modified Library. (It is understood
+ that the user who changes the contents of definitions files in the
+ Library will not necessarily be able to recompile the application
+ to use the modified definitions.)
+
+ b) Use a suitable shared library mechanism for linking with the
+ Library. A suitable mechanism is one that (1) uses at run time a
+ copy of the library already present on the user's computer system,
+ rather than copying library functions into the executable, and (2)
+ will operate properly with a modified version of the library, if
+ the user installs one, as long as the modified version is
+ interface-compatible with the version that the work was made with.
+
+ c) Accompany the work with a written offer, valid for at
+ least three years, to give the same user the materials
+ specified in Subsection 6a, above, for a charge no more
+ than the cost of performing this distribution.
+
+ d) If distribution of the work is made by offering access to copy
+ from a designated place, offer equivalent access to copy the above
+ specified materials from the same place.
+
+ e) Verify that the user has already received a copy of these
+ materials or that you have already sent this user a copy.
+
+ For an executable, the required form of the "work that uses the
+Library" must include any data and utility programs needed for
+reproducing the executable from it. However, as a special exception,
+the materials to be distributed need not include anything that is
+normally distributed (in either source or binary form) with the major
+components (compiler, kernel, and so on) of the operating system on
+which the executable runs, unless that component itself accompanies
+the executable.
+
+ It may happen that this requirement contradicts the license
+restrictions of other proprietary libraries that do not normally
+accompany the operating system. Such a contradiction means you cannot
+use both them and the Library together in an executable that you
+distribute.
+\f
+ 7. You may place library facilities that are a work based on the
+Library side-by-side in a single library together with other library
+facilities not covered by this License, and distribute such a combined
+library, provided that the separate distribution of the work based on
+the Library and of the other library facilities is otherwise
+permitted, and provided that you do these two things:
+
+ a) Accompany the combined library with a copy of the same work
+ based on the Library, uncombined with any other library
+ facilities. This must be distributed under the terms of the
+ Sections above.
+
+ b) Give prominent notice with the combined library of the fact
+ that part of it is a work based on the Library, and explaining
+ where to find the accompanying uncombined form of the same work.
+
+ 8. You may not copy, modify, sublicense, link with, or distribute
+the Library except as expressly provided under this License. Any
+attempt otherwise to copy, modify, sublicense, link with, or
+distribute the Library is void, and will automatically terminate your
+rights under this License. However, parties who have received copies,
+or rights, from you under this License will not have their licenses
+terminated so long as such parties remain in full compliance.
+
+ 9. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Library or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
+modifying or distributing the Library (or any work based on the
+Library), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Library or works based on it.
+
+ 10. Each time you redistribute the Library (or any work based on the
+Library), the recipient automatically receives a license from the
+original licensor to copy, distribute, link with or modify the Library
+subject to these terms and conditions. You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties with
+this License.
+\f
+ 11. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Library at all. For example, if a patent
+license would not permit royalty-free redistribution of the Library by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Library.
+
+If any portion of this section is held invalid or unenforceable under any
+particular circumstance, the balance of the section is intended to apply,
+and the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+ 12. If the distribution and/or use of the Library is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Library under this License may add
+an explicit geographical distribution limitation excluding those countries,
+so that distribution is permitted only in or among countries not thus
+excluded. In such case, this License incorporates the limitation as if
+written in the body of this License.
+
+ 13. The Free Software Foundation may publish revised and/or new
+versions of the Lesser General Public License from time to time.
+Such new versions will be similar in spirit to the present version,
+but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Library
+specifies a version number of this License which applies to it and
+"any later version", you have the option of following the terms and
+conditions either of that version or of any later version published by
+the Free Software Foundation. If the Library does not specify a
+license version number, you may choose any version ever published by
+the Free Software Foundation.
+\f
+ 14. If you wish to incorporate parts of the Library into other free
+programs whose distribution conditions are incompatible with these,
+write to the author to ask for permission. For software which is
+copyrighted by the Free Software Foundation, write to the Free
+Software Foundation; we sometimes make exceptions for this. Our
+decision will be guided by the two goals of preserving the free status
+of all derivatives of our free software and of promoting the sharing
+and reuse of software generally.
+
+ NO WARRANTY
+
+ 15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
+WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
+OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY
+KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
+LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
+THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
+WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
+AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
+FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
+CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
+RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+\f
+ How to Apply These Terms to Your New Libraries
+
+ If you develop a new library, and you want it to be of the greatest
+possible use to the public, we recommend making it free software that
+everyone can redistribute and change. You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
+
+ To apply these terms, attach the following notices to the library. It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the library's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Also add information on how to contact you by electronic and paper mail.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ <signature of Ty Coon>, 1 April 1990
+ Ty Coon, President of Vice
+
+That's all there is to it!
+
+
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::analysismodules::Freevolume.
+ *
+ * \author Titov Anatoly <Wapuk-cobaka@yandex.ru>
+ * \ingroup module_trajectoryanalysis
+ */
+
+#include <iostream>
+#include <chrono>
+#include <omp.h>
+#include <thread>
+#include <string>
+
+#include <gromacs/trajectoryanalysis.h>
+#include <gromacs/pbcutil/pbc.h>
+#include <gromacs/pbcutil/rmpbc.h>
+#include <gromacs/utility/smalloc.h>
+#include <gromacs/math/vectypes.h>
+#include <gromacs/math/vec.h>
+#include <gromacs/math/do_fit.h>
+
+#define MAX_NTRICVEC 12
+
+using namespace gmx;
+
+using gmx::RVec;
+
+struct node {
+ short int n;
+ RVec r;
+ bool yep;
+};
+
+void make_graph(int mgwi_natoms, rvec *mgwi_x, std::vector< std::vector< node > > &mgwi_graph)
+{
+ mgwi_graph.resize(mgwi_natoms);
+ for (int i = 0; i < mgwi_natoms; i++) {
+ mgwi_graph[i].resize(mgwi_natoms);
+ }
+ for (int i = 0; i < mgwi_natoms; i++) {
+ for (int j = 0; j < mgwi_natoms; j++) {
+ rvec_sub(mgwi_x[i], mgwi_x[j], mgwi_graph[i][j].r);
+ mgwi_graph[i][j].n = 0;
+ }
+ }
+}
+
+void update_graph(std::vector< std::vector< node > > &ugwi_graph, rvec *ugwi_x, long double ugwi_epsi) {
+ rvec ugwi_temp;
+ int ugwi_for = ugwi_graph.size();
+ for (int i = 0; i < ugwi_for; i++) {
+ for (int j = i; j < ugwi_for; j++) {
+ rvec_sub(ugwi_x[i], ugwi_x[j], ugwi_temp);
+ rvec_dec(ugwi_temp, ugwi_graph[i][j].r.as_vec());
+ if (norm(ugwi_temp) <= ugwi_epsi) {
+ if (i == j) {
+ ugwi_graph[i][j].n++;
+ }
+ else {
+ ugwi_graph[i][j].n++;
+ ugwi_graph[j][i].n++;
+ }
+ }
+ }
+ }
+}
+
+void check_domains(long double cd_delta, int cd_frames, std::vector< std::vector< std::vector< node > > > &cd_graph) {
+ int cd_for1 = cd_graph.size(), cd_for2 = cd_graph[1].size();
+ for (int k = 0; k < cd_for1; k++) {
+ for (int i = 0; i < cd_for2; i++) {
+ for (int j = 0; j < cd_for2; j++) {
+ if (cd_graph[k][i][j].n >= cd_frames * cd_delta) {
+ cd_graph[k][i][j].yep = true;
+ }
+ else {
+ cd_graph[k][i][j].yep = false;
+ }
+ }
+ }
+ }
+}
+
+void find_domain_sizes(std::vector< std::vector< std::vector< node > > > fds_graph, std::vector< std::vector< int > > &fds_domsizes) {
+ fds_domsizes.resize(fds_graph.size());
+ int fds_for1 = fds_graph.size(), fds_for2 = fds_graph[1].size();
+ for (int i = 0; i < fds_for1; i++) {
+ fds_domsizes[i].resize(fds_for2, 0);
+ for (int j = 0; j < fds_for2; j++) {
+ for (int k = 0; k < fds_for2; k++) {
+ if (fds_graph[i][j][k].yep) {
+ fds_domsizes[i][j]++;
+ }
+ }
+ }
+ }
+}
+
+void get_maxsized_domain(std::vector< int > &gmd_max_d, std::vector< std::vector< std::vector< node > > > gmd_graph, std::vector< std::vector< int > > gmd_domsizes) {
+ int gmd_number1 = 0, gmd_number2 = 0;
+ int gmd_for1 = gmd_domsizes.size(), gmd_for2 = gmd_domsizes[0].size(), gmd_for3 = gmd_graph[1][1].size();
+ for (int i = 0; i < gmd_for1; i++) {
+ for (int j = 0; j < gmd_for2; j++) {
+ if (gmd_domsizes[i][j] >= gmd_domsizes[gmd_number1][gmd_number2]) {
+ gmd_number1 = i;
+ gmd_number2 = j;
+ }
+ }
+ }
+ gmd_max_d.resize(0);
+ for (int i = 0; i < gmd_for3; i++) {
+ if (gmd_graph[gmd_number1][gmd_number2][i].yep) {
+ gmd_max_d.push_back(i);
+ }
+ }
+}
+
+void delete_domain_from_graph(std::vector< std::vector< std::vector< node > > > &ddf_graph, std::vector< int > ddf_domain) {
+ int ddfg_for1 = ddf_domain.size(), ddfg_for2 = ddf_graph.size(), ddfg_for3 = ddf_graph[1].size();
+ for (int i = 0; i < ddfg_for1; i++) {
+ for (int k = 0; k < ddfg_for2; k++) {
+ for (int j = 0; j < ddfg_for3; j++) {
+ if (ddf_graph[k][ddf_domain[i]][j].yep) {
+ ddf_graph[k][ddf_domain[i]][j].yep = false;
+ }
+ if (ddf_graph[k][j][ddf_domain[i]].yep) {
+ ddf_graph[k][j][ddf_domain[i]].yep = false;
+ }
+ }
+ }
+ }
+}
+
+bool check_domsizes(std::vector< std::vector< int > > cd_domsizes, int cd_domain_min_size) {
+ int cd_for1 = cd_domsizes.size(), cd_for2 = cd_domsizes[0].size();
+ for (int i = 0; i < cd_for1; i++) {
+ for (int j = 0; j < cd_for2; j++) {
+ if (cd_domsizes[i][j] >= cd_domain_min_size) {
+ return true;
+ }
+ }
+ }
+ return false;
+}
+
+void print_domains(std::vector< std::vector< int > > pd_domains, std::vector< int > index, std::string fnNdx_) {
+ FILE *fpNdx_;
+ fpNdx_ = std::fopen(fnNdx_.c_str(), "w+");
+ int write_count;
+ for (int i = 0; i < pd_domains.size(); i++) {
+ std::fprintf(fpNdx_, "[domain_%d]\n", i + 1);
+ write_count = 0;
+ for (int j = 0; j < pd_domains[i].size(); j++) {
+ write_count++;
+ if (write_count > 20) {
+ write_count -= 20;
+ std::fprintf(fpNdx_, "\n");
+ }
+ std::fprintf(fpNdx_, "%5d ", index[pd_domains[i][j]] + 1);
+ }
+ std::fprintf(fpNdx_,"\n\n");
+ }
+ std::fprintf(fpNdx_,"\n");
+ std::fclose(fpNdx_);
+}
+
+
+/*! \brief
+ * Class used to compute free volume in a simulations box.
+ *
+ * Inherits TrajectoryAnalysisModule and all functions from there.
+ * Does not implement any new functionality.
+ *
+ * \ingroup module_trajectoryanalysis
+ */
+class Domains : public TrajectoryAnalysisModule
+{
+ public:
+
+ Domains();
+ virtual ~Domains();
+
+ //! Set the options and setting
+ virtual void initOptions(IOptionsContainer *options,
+ TrajectoryAnalysisSettings *settings);
+
+ //! First routine called by the analysis framework
+ // virtual void initAnalysis(const t_trxframe &fr, t_pbc *pbc);
+ virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top);
+
+ virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
+ const t_trxframe &fr);
+
+ //! Call for each frame of the trajectory
+ // virtual void analyzeFrame(const t_trxframe &fr, t_pbc *pbc);
+ virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata);
+
+ //! Last routine called by the analysis framework
+ // virtual void finishAnalysis(t_pbc *pbc);
+ virtual void finishAnalysis(int nframes);
+
+ //! Routine to write output, that is additional over the built-in
+ virtual void writeOutput();
+
+ private:
+
+ std::string fnNdx_;
+
+ std::vector< std::vector< std::vector< node > > > graph;
+
+ std::vector< std::vector< int > > domains;
+ std::vector< std::vector< int > > domsizes;
+
+ std::vector< int > index;
+ std::vector< int > numbers;
+ std::vector< std::vector < RVec > > trajectory;
+ Selection selec;
+ int frames = 0;
+ int domain_min_size = 5; // should be selectable
+
+ real **w_rls;
+ int bone;
+ double delta = 0.90; //0.95 // should be selectable
+ double epsi = 0.15; //0.3 колебания внутри домена // should be selectable
+
+ int domains_ePBC;
+ // Copy and assign disallowed by base.
+};
+
+Domains::Domains(): TrajectoryAnalysisModule()
+{
+}
+
+Domains::~Domains()
+{
+}
+
+void
+Domains::initOptions(IOptionsContainer *options,
+ TrajectoryAnalysisSettings *settings)
+{
+ static const char *const desc[] = {
+ "[THISMODULE] to be done"
+ };
+ // Add the descriptive text (program help text) to the options
+ settings->setHelpText(desc);
+ // Add option for selecting a subset of atoms
+ options->addOption(SelectionOption("select")
+ .store(&selec).required()
+ .description("Atoms that are considered as part of the excluded volume"));
+ // Add option for output file name
+ options->addOption(FileNameOption("on").filetype(eftIndex).outputFile()
+ .store(&fnNdx_).defaultBasename("domains")
+ .description("Index file from the domains"));
+ // Add option for etalon_frame constant
+ options->addOption(gmx::IntegerOption("dms")
+ .store(&domain_min_size)
+ .description("minimum domain size"));
+ // Add option for epsi constant
+ options->addOption(DoubleOption("epsilon")
+ .store(&epsi)
+ .description("thermal vibrations' constant"));
+ // Add option for delta constant
+ options->addOption(DoubleOption("delta")
+ .store(&delta)
+ .description("domain membership probability"));
+ // Control input settings
+ settings->setFlags(TrajectoryAnalysisSettings::efNoUserPBC);
+ settings->setPBC(true);
+}
+
+void
+Domains::initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top)
+{
+ domains_ePBC = top.ePBC();
+}
+
+void
+Domains::initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
+ const t_trxframe &fr)
+{
+ t_pbc pbc;
+ t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
+ matrix boxx;
+ copy_mat(fr.box, boxx);
+ if (ppbc != NULL) {
+ set_pbc(ppbc, domains_ePBC, boxx);
+ }
+ ConstArrayRef< int > atomind = selec.atomIndices();
+ index.resize(0);
+ for (ConstArrayRef<int>::iterator ai = atomind.begin(); (ai < atomind.end()); ai++) {
+ index.push_back(*ai);
+ }
+ trajectory.resize(2);
+ trajectory[0].resize(selec.atomCount());
+
+ for (int i = 0; i < selec.atomCount(); i++) {
+ trajectory[0][i] = fr.x[index[i]];
+ }
+
+ bone = index.size() - domain_min_size + 1;
+ graph.resize(bone);
+ snew(w_rls, bone);
+ for (int i = 0; i < bone; i++) {
+ snew(w_rls[i], index.size());
+ for (int j = 0; j < index.size(); j++) {
+ if (j >= i && j <= i + domain_min_size - 1) {
+ w_rls[i][j] = 1;
+ } else {
+ w_rls[i][j] = 0;
+ }
+ }
+ rvec *etalon;
+ snew(etalon, index.size());
+ for (int j = 0; j < index.size(); j++) {
+ copy_rvec(trajectory[0][j].as_vec(), etalon[j]);
+ }
+ reset_x(index.size(), NULL, index.size(), NULL, etalon, w_rls[i]);
+ make_graph(index.size(), etalon, graph[i]);
+ sfree(etalon);
+ }
+ trajectory[1].resize(index.size());
+}
+
+void
+Domains::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata)
+{
+ for (int i = 0; i < index.size(); i++) {
+ trajectory[1][i] = fr.x[index[i]];
+ }
+ frames++;
+
+ #pragma omp parallel
+ {
+ #pragma omp for schedule(dynamic)
+ for (int j = 0; j < bone; j++) {
+ rvec *etalon, *traj;
+ snew(etalon, index.size());
+ for (int k = 0; k < index.size(); k++) {
+ copy_rvec(trajectory[0][k].as_vec(), etalon[k]);
+ }
+ snew(traj, index.size());
+ for (int k = 0; k < index.size(); k++) {
+ copy_rvec(trajectory[1][k].as_vec(), traj[k]);
+ }
+ reset_x(index.size(), NULL, index.size(), NULL, etalon, w_rls[j]);
+ reset_x(index.size(), NULL, index.size(), NULL, traj, w_rls[j]);
+ do_fit(index.size(), w_rls[j], etalon, traj);
+ update_graph(graph[j], traj, epsi);
+ sfree(etalon);
+ sfree(traj);
+ }
+ }
+ std::cout << "frame: " << frames << " analyzed\n";
+}
+
+//domains -s '/home/toluk/Develop/samples/reca_rd/reca_rd.mono.tpr' -f '/home/toluk/Develop/samples/reca_rd/reca_rd.mono.xtc' -select 'name CA'
+//domains -s '/home/toluk/Develop/samples/banana_phone/pgk.md.non-sol.tpr' -f '/home/toluk/Develop/samples/banana_phone/pgk.md.non-sol.10th.xtc' -select 'name CA'
+//domains -s '/home/toluk/Data/reca_rd/reca_rd.mono.tpr' -f '/home/toluk/Data/reca_rd/reca_rd.mono.xtc' - select 'name CA'
+
+void
+Domains::finishAnalysis(int nframes)
+{
+ frames -= 1;
+
+ std::cout << "final cheking\n";
+ check_domains(delta, frames, graph);
+
+ std::cout << "finding domains' sizes\n";
+ find_domain_sizes(graph, domsizes);
+
+ std::cout << "finding domains\n";
+ std::vector< int > a;
+ a.resize(0);
+ while (check_domsizes(domsizes, domain_min_size)) {
+ domains.push_back(a);
+ get_maxsized_domain(domains.back(), graph, domsizes);
+ delete_domain_from_graph(graph, domains.back());
+ domsizes.resize(0);
+ find_domain_sizes(graph, domsizes);
+ }
+ for (int i = 0; i < bone; i++) {
+ sfree(w_rls[i]);
+ }
+ sfree(w_rls);
+}
+
+void
+Domains::writeOutput()
+{
+ std::cout << "making output file\n";
+ print_domains(domains, index, fnNdx_); // see function for details | numbers from index
+ std::cout << "\n END \n";
+}
+
+
+/*! \brief
+ * The main function for the analysis template.
+ */
+int
+main(int argc, char *argv[])
+{
+ return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<Domains>(argc, argv);
+}
biod.pnpi.spb.ru / alexxy / gromacs-fitng.git / commitdiff