# Getting Started¶

This documentation describes the software package PHCpack.

This work is licensed under a Creative Commons Attribution-Share Alike 3.0 License.

## What is PHCpack?¶

PHCpack implements a collection of algorithms to solve polynomial systems by homotopy continuation methods.

On input is a sequence of polynomials in several variables, on output are the solutions to the polynomial system given on input. The computational complexity of this problem is #P-hard because of the exponential growth of the number of solutions as the number of input polynomials increases. For example, ten polynomials of degree two may intersect in 1,024 isolated points (that is two to the power ten). Twenty quadratic polynomials may lead to 1,048,576 solutions (that is 1,024 times 1,024). So it is not too difficult to write down small input sequences that lead to a huge output.

Even as the computation of the total number of solutions may take a long time, numerical homotopy continuation methods have the advantage that they compute one solution after the other. A homotopy is a family of polynomial systems, connecting the system we want to solve with an easier to solve system, which is called the start system. Numerical continuation methods track the solution paths starting at known solutions of an easier system to the system we want to solve. We have an optimal homotopy if every path leads to a solution, that is: there are no divergent paths.

PHCpack offers optimal homotopies for systems that resemble linear-product structures, for geometric problems in enumerative geometry, and for sparse polynomial systems with sufficiently generic choices of the coefficients. While mathematically this sounds all good, most systems arising in practical applications have their own peculiar structure and so most homotopies will lead to diverging solution paths. In general, a polynomial system may have solution sets of many different dimensions, which renders the solving process challenging but at the same time still very interesting.

Version 1.0 of PHCpack was archived as Algorithm 795 by ACM Transactions on Mathematical Software. PHCpack is open source and free software which gives any user the same rights as in free speech. You can redistribute PHCpack and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 of the License.

## Downloading and Installing¶

Executable versions of the program for various machine architectures and operating systems are available via <http://www.math.uic.edu/~jan/download.html>.

For the Windows operating systems, the
executable version of phc is in the file `phc.exe`

and is available for download in its uncompressed format.
Using the plain version of phc on a Windows system
requires the opening of a command prompt window
and typing `phc`

at the prompt.
To run `phc`

from any folder, different from the folder where
you save `phc.exe`

, you have to change the environment variable `path`

.
On Windows 10, type `env`

in the Search window and select
`Edit the system environment variables`

under the `Settings`

.
After this selection, click on the `Environment Variables...`

button
and select `Path`

from the `System Variables`

.
Via the `Edit`

button you can insert the name of the folder where
you saved the file `phc.exe`

. Alternatively, you could of course
save the `phc.exe`

in a folder which is already on your path.

For Mac OS X and Linux versions,
the executable is tarred and gzipped.
If the downloaded file is saved as `*phcv2_4p.tar.gz`

,
then the following commands to unzip and untar the downloaded file
can be typed at the command prompt:

```
gunzip *phcv2_4p.tar.gz
tar xpf *phcv2_4p.tar
```

If all went well, typing `./phc`

at the command prompt should bring
up the welcome message and the screen with available options.

The executable `phc`

gives access to almost all the functionality
of PHCpack, including the multitasking capabilities
for shared memory parallelism
on multicore processors.
For other parallel capabilities, such
as distributed memory parallelism with
the Message Passing Interface (MPI)
and massive parallelism on
a Graphics Processing Unit (GPU),
one will need to compile the source code.

## Compiling from Source¶

The source code is under version control
at github,
at <https://github.com/janverschelde/PHCpack>.
To compile the source code, the gnu-ada compiler is needed.
Free binary versions of the gnu-ada compiler
are available at <http://libre.adacore.com>.
One does not need to be superuser to install the gnu-ada compiler.
The directory `Objects`

in the
source code provides makefiles for Linux, Mac OS X, and Windows
operating systems.

When compiling from source, note that since version 2.4.35, the quad double library QDlib must be installed. Alternatively, one can also compile the QD library in a user account and then adjust the makefiles for the location of the header files and the archive qdlib.a. The makefile for Windows provides an example of a compilation of the QD library under a user account. On Linux systems, the qdlib.a must have been compiled with the -fPIC option for the shared object file for the C extension module of phcpy.

Alternatively, the executable phc can be built without the
dependency on the installed QDlib. The makefile contains
the instructions for the `make phc_noqd`

compilation.
For this compilation, a working version of the gnu-ada compiler
should be available at the front of the execution path.

The software has been compiled with many versions of gcc
on Linux, Mac OS X, and Windows computers.
While the software does not require any particular version of gcc,
the C, C++, and Ada code must be compiled with the *same* version of gcc.
One cannot link object code produced by, for example g++ 4.9.3,
with other object code compiled by another version of gcc,
for example gcc 4.9.2.

## Project History¶

The software originated in the development of new homotopy algorithms to solve polynomial systems. The main novelty of the first release of the sources was the application of polyhedral homotopies in the blackbox solver. Polyhedral homotopies are generically optimal for sparse polynomial systems. Although the number of solutions may grow exponentially in the number of equations, variables, and degrees, for systems where the coefficients are sufficiently generic, every solution path defined by a polyhedral homotopy will lead to one isolated solution.

Version 2.0 of the code implemented SAGBI and Pieri homotopies to solve problem in enumerative geometry. A classical problem in Schubert calculus is the problem of the two lines that meet four general lines in 3-space. Pieri homotopies are generically optimal to compute all solutions to such geometric problems. They solve the output pole placement problem in linear systems control. With message passing, parallel versions of the Pieri homotopies lead to good speedups on parallel distributed memory computers.

Starting with version 2.0 was the gradual introduction of new homotopies to deal with positive dimensional solution sets. Cascades of homotopies provide generic points on every solution set, at every dimension. After the application of cascade homotopies to compute generic points on all equidimensional components, the application of monodromy loops with the linear trace stop test classifies the generic points on the equidimensional component into irreducible components. This leads to a numerical irreducible decomposition of the solution set of a polynomial system. Cascade of homotopies are the top down method. A bottom up method applies diagonal homotopies to intersect positive dimensional solution sets in an equation-by-equation solver.

To deal with singular solutions of polynomial systems, the deflation method was added in version 2.3. Version 2.3 was quickly followed by a bug release 2.3.01 and subsequently by many more quick releases. The introduction of the fast mixed volume calculator MixedVol in 2.3.13 was followed by capabilities to compute stable mixed volumes in 2.3.31, and an upgrade of the blackbox solver in version 2.3.34.

Shared memory multitasking provided the option -t, followed by the number of tasks, to speedup the path tracking. Our main motivation of parallelism is to offset the extra cost of multiprecision arithmetic, in particular double double and quad double arithmetic. Marking a milestone after one hundred quick releases, version 2.4 provided path tracking methods on graphics processing units. A collection of Python scripts defines a simple web interface to the blackbox solver and the path trackers, enabling the solution of polynomial systems in the cloud. DEMiCs applies dynamic enumeration for all mixed cells and computes the mixed volume at a faster pace than MixedVol. Since version 2.4.53, DEMiCs is distributed with PHCpack.

## phcpy: An Application Programming Interface to PHCpack¶

Because code development on PHCpack has taken a very long time, looking at the code may be a bit too overwhelming at first. A good starting point could be the Python interface and in particular phcpy, with documentation at <http://www.math.uic.edu/~jan/phcpy_doc_html/index.html>.

The main executable `phc`

built by the code in PHCpack
is called at the command line with options to invoke specific tools
and with file names as arguments in which the input and output data goes.
In contrast, the scripting interface replaces the files with persistent
objects and instead of selecting options from menus, the user runs scripts.

## References¶

PHCpack relies for its fast mixed volume computation on MixedVol and DEMiCs. For its double double and quad double arithmetic, there is QDlib which is integrated in PHCpack. Pointers to the literature are mentioned below.

- N. Bliss, J. Sommars, J. Verschelde and X. Yu:
**Solving polynomial systems in the cloud with polynomial homotopy continuation.**In*Computer Algebra in Scientific Computing, 17th International Workshop, CASC 2015, Aachen, Germany*, edited by V.P. Gerdt, W. Koepf, E.W. Mayr, and E.V. Vorozhtsov. Volume 9301 of*Lecture Notes in Computer Science*, pages 87-100, Springer-Verlag, 2015. - T. Gao, T. Y. Li, M. Wu:
**Algorithm 846: MixedVol: a software package for mixed-volume computation.***ACM Transactions on Mathematical Software*, 31(4):555-560, 2005. - E. Gross, S. Petrovic, and J. Verschelde:
**PHCpack in Macaulay2.***The Journal of Software for Algebra and Geometry: Macaulay2*, 5:20-25, 2013. - Y. Guan and J. Verschelde:
**PHClab: A MATLAB/Octave interface to PHCpack.**In*Software for Algebraic Geometry*, volume 148 of the IMA volumes in Mathematics and its Applications, edited by M.E. Stillman, N. Takayama, and J. Verschelde, pages 15-32, Springer-Verlag, 2008. - Y. Hida, X.S. Li, and D.H. Bailey:
**Algorithms for quad-double precision floating point arithmetic.**In*15th IEEE Symposium on Computer Arithmetic (Arith-15 2001)*, 11-17 June 2001, Vail, CO, USA, pages 155-162. IEEE Computer Society, 2001. Shortened version of Technical Report LBNL-46996. - A. Leykin and J. Verschelde:
**PHCmaple: A Maple Interface to the Numerical Homotopy Algorithms in PHCpack.**In the*Proceedings of the Tenth International Conference on Applications of Computer Algebra (ACA‘2004)*, edited by Q. N. Tran, pages 139-147, 2004. - A. Leykin and J. Verschelde:
**Interfacing with the Numerical Homotopy Algorithms in PHCpack.**In the*Proceedings of ICMS 2006, LNCS 4151*, edited by A. Iglesias and N. Takayama, pages 354-360, Springer-Verlag, 2006. - T. Mizutani and A. Takeda.
**DEMiCs: A software package for computing the mixed volume via dynamic enumeration of all mixed cells.**In*Software for Algebraic Geometry*, edited by M.E. Stillman, N. Takayama, and J. Verschelde, volume 148 of The IMA Volumes in Mathematics and its Applications, pages 59-79. Springer-Verlag, 2008. - T. Mizutani, A. Takeda, and M. Kojima.
**Dynamic enumeration of all mixed cells.***Discrete Comput. Geom.*37(3):351-367, 2007. - M. Lu., B. He and Q. Luo.
**Supporting extended precision on graphics processors.**In the*Proceedings of the Sixth International Workshop on Data Management on New Hardware (DaMoN 2010), June 7, 2010, Indianapolis, Indiana*, edited by A. Ailamaki and P.A. Boncz, pages 19-26, 2010. - J. Otto, A. Forbes, and J. Verschelde.
**Solving Polynomial Systems with phcpy.**In the*Proceedings of the 18th Python in Science Conference (SciPy 2019)*, edited by Chris Calloway, David Lippa, Dillon Niederhut and David Shupe, pages 58-64, 2019. - K. Piret and J. Verschelde:
**Sweeping Algebraic Curves for Singular Solutions.***Journal of Computational and Applied Mathematics*, 234(4): 1228-1237, 2010. - A. J. Sommese, J. Verschelde, and C. W. Wampler.
**Numerical irreducible decomposition using PHCpack.**In*Algebra, Geometry, and Software Systems*, edited by M. Joswig and N. Takayama, pages 109-130. Springer-Verlag, 2003. - J. Verschelde:
**Algorithm 795: PHCpack: A general-purpose solver for polynomial systems by homotopy continuation.***ACM Transactions on Mathematical Software*, 25(2):251–276, 1999. - J. Verschelde:
**Polynomial homotopy continuation with PHCpack.***ACM Communications in Computer Algebra*, 44(4):217-220, 2010. - J. Verschelde:
**Modernizing PHCpack through phcpy.**In the*Proceedings of the 6th European Conference on Python in Science (EuroSciPy 2013)*, edited by Pierre de Buyl and Nelle Varoquaux, pages 71-76, 2014, available at <http://arxiv.org/abs/1310.0056>. - J. Verschelde and G. Yoffe.
**Polynomial homotopies on multicore workstations.**In the*Proceedings of the 4th International Workshop on Parallel Symbolic Computation (PASCO 2010), July 21-23 2010, Grenoble, France*, edited by M.M. Maza and J.-L. Roch, pages 131–140. ACM, 2010. - J. Verschelde and X. Yu:
**Polynomial Homotopy Continuation on GPUs.***ACM Communications in Computer Algebra*, 49(4):130-133, 2015. - J. Verschelde:
**A Blackbox Polynomial System Solver on Parallel Shared Memory Computers.**In the*Proceedings of the 20th International Workshop on Computer Algebra in Scientific Computing (CASC 2018)*, edited by V.P. Gerdt, W. Koepf, W.M. Seiler, and E.V. Vorozhtsov, volume 11077 of Lecture Notes in Computer Science, pages 361-375, Springer-Verlag, 2018.

## Users¶

To demonstrate the relevance of the software, the first version of the software was released with a collection of about eighty different polynomial systems, collected from the literature. This section points to a different collection of problems, problems that have been solved by users of the software, without intervention of its developers.

The papers listed below report the use of PHCpack in the fields of algebraic statistics, communication networks, geometric constraint solving, real algebraic geometry, computation of Nash equilibria, signal processing, magnetism, mechanical design, computational geometry, computer vision, optimal control, image processing, pattern recognition, global optimization, and computational physics:

- M. Abdullahi, B.I. Mshelia, and S. Hamma:
**Solution of polynomial system using PHCpack**.*Journal of Physical Sciences and Innovation*, 4:44-53, 2012. - Michael F. Adamer and Martin Helmer:
**Complexity of model testing for dynamical systems with toric steady states**.*Advances in Applied Mathematics*110: 42-75, 2019. - Min-Ho Ahn, Dong-Oh Nam and Chung-Nim Lee:
**Self-Calibration with Varying Focal Lengths Using the Infinity Homography**. In*Proceedings of the 4th Asian Conference on Computer Vision*(ACCV2000), pages 140-145, 2000. - Carlos Amendola, Nathan Bliss, Isaac Burke,
Courtney R. Gibbons, Martin Helmer, Serkan Hosten,
Evan D. Nash, Jose Israel Rodriguez, Daniel Smolkin:
**The maximum likelihood degree of toric varieties.***Journal of Symbolic Computation*, article in Press, 2018. - Gianni Amisano and Oreste Tristani:
**Exact likelihood computation for nonlinear DSGE models with heteroskedastic innovations**.*Journal of Economic Dynamics and Control*35:2167-2185, 2011. - D. Arzelier, C. Louembet, A. Rondepierre, and M. Kara-Zaitri:
**A New Mixed Iterative Algorithm to Solve the Fuel-Optimal Linear Impulsive Rendezvous Problem.***Journal of Optimization Theory and Applications*, 2013. - E. Bartzos, I. Emiris, J. Legersky, and E. Tsigaridas:
**On the maximal number of real embeddings of spatial minimally rigid graphs.**In*Proceedings of the 2018 International Symposium on Symbolic and Algebraic Computation (ISSAC 2018)*, pages 55-62, ACM 2018. - Bassi, I.G., Abdullahi Mohammed, and Okechukwu C.E.:
**Analysis Of Solving Polynomial Equations Using Homotopy Continuation Method**.*International Journal of Engineering Research & Technology (IJERT)*2(8):1401-1411, 2013. - Dmitry Batenkov:
**Accurate solution of near-colliding Prony systems via decimation and homotopy continuation**.*Theoretical Computer Science*681:1-232, 2017. - Daniel J. Bates and Frank Sottile:
**Khovanskii-Rolle Continuation for Real Solutions**.*Foundations of Computational Mathematics*11:563-587, 2011. - Jahan Bayat and Carl D. Crane III:
**Closed-Form Equilibrium Analysis of Planar Tensegrity Mechanisms**. In*2006 Florida Conference on Recent Advances in Robotics*, FCRAR 2006. - Genevieve Belanger, Kristjan Kannike, Alexander Pukhov, and Martti Raidal:
**Minimal semi-annihilating Z_n scalar dark matter**.*Journal of Cosmology and Astroparticle Physics*, June 2014 (Open Access). - Ivo W.M. Bleylevens, Michiel E. Hostenbach, and Ralf L.M. Peeters:
**Polynomial Optimization and a Jacobi-Davidson type method for commuting matrices**,*Applied Mathematics and Computation*224(1): 564-580, 2013. - Guy Bresler, Dustin Cartwright, David Tse:
**Feasibility of Interference Alignment for the MIMO interference channel**.*IEEE Transactions on Information Theory*60(9):5573-5586, 2014. - M.-L. G. Buot and D. St. P. Richards:
**Counting and Locating the Solutions of Polynomial Systems of Maximum Likelihood Equations I**.*Journal of Symbolic Computation*41(2): 234-244, 2005. - Max-Louis G. Buot, Serkan Hosten and Donald St. P. Richards:
**Counting and locating the solutions of polynomial systems of maximum likelihood equations, II: The Behrens-Fisher problem**.*Statistica Sinica*17(4):1343-1354, 2007. - Enric Celaya, Tom Creemers, Lluis Ros:
**Exact interval propagation for the efficient solution of position analysis problems on planar linkages**.*Mechanism and Machine Theory*54: 116-131, 2012. - Zachary Charles and Nigel Boston:
**Exploiting algebraic structure in global optimization and the Belgian chocolate problem**.*Journal of Global Optimization*72(2): 241-254, 2018. - Tom Creemers, Josep M. Porta, Lluis Ros, and Federico Thomas:
**Fast Multiresolutive Approximations of Planar Linkage Configuration Spaces**.*IEEE 2006 International Conference on Robotics and Automation.* - Marc Culler and Nathan M. Dunfield:
**Orderability and Dehn filling.***Geometry and Topology*22: 1405-1457, 2018. - R.S. Datta:
**Using Computer Algebra To Compute Nash Equilibria**. In*Proceedings of the 2003 International Symposium on Symbolic and Algebraic Computation (ISSAC 2003)*, pages 74-79, ACM 2003. - R.S. Datta:
**Finding all Nash equilibria of a finite game using polynomial algebra**.*Economic Theory*42(1):55-96, 2009. - B.H. Dayton:
**Numerical Local Rings and Local Solution of Nonlinear Systems**. In*Proceedings of the 2007 International Workshop on Symbolic-Numeric Computation (SNC‘07)*, pages 79-86, ACM 2007. - Max Demenkov:
**Estimating region of attraction for polynomial vector fields by homotopy methods**.*ACM Communications in Computer Algebra*46(3):84-85, 2012. - Max Demenkov:
A Matlab Tool for Regions of Attraction Estimation
via Numerical Algebraic Geometry.</B>
In the
*2015 International Conference on Mechanics - Seventh Polyakhov’s Reading*, February 2-6, 2015, Russia, Saint Petersburg State University, Proceedings Edited by A.A. Tikhonov. IEEE 2015. - Ian H. Dinwoodie, Emily Gamundi, and Ed Mosteig:
**Multiple Solutions for Blocking Probabilities in Asymmetric Networks**.*Open Systems and Information Dynamics*12(3):273-288, 2005. - Csaba Domokos and Zoltan Kato:
**Parametric Estimation of Affine Deformations of Planar Shapes**.*Pattern Recognition*, 2009. In press. - C. Durand and C.M. Hoffmann:
**Variational Constraints in 3D**. In*Proceedings of the International Conference on Shape Modeling and Applications*, Aizu-Wakamatsu, Japan, pages 90-98, IEEE Computer Society, 1999. - C. Durand and C.M. Hoffmann:
**A systematic framework for solving geometric constraints analytically**.*Journal of Symbolic Computation*30(5):493-520, 2000. - I.Z. Emiris, E. Tsigaridas, G. Tzoumas:
**The predicates for the Voronoi diagram of ellipses**. In*Proc. ACM Symp. Comput. Geom.*2006. - Jonathan P. Epperlein and Bassam Bamieh:
**A Frequency Domain Method for Optimal Periodic Control**. 2012 American Control Conference (ACC), pages 5501-5506, IEEE 2012. - F. Ferrari:
**On the geometry of super Yang-Mills theories: phases and irreducible polynomials**.*Journal of High Energy Physics*1, paper 26, 2009. - Jaime Gallardo-Alvarado:
**A simple method to solve the forward displacement analysis of the general six-legged parallel manipulator**.*Robotics and Computer-Integrated Manufacturing*30:55-61, 2014. - Jaime Gallardo-Alvarado:
**Gough’s Tyre Testing Machine**. Chapter 12 of*Kinematic Analysis of Parallel Manipulators by Algebraic Screw Theory*, pages 255-280, Springer-Verslag, 2016. - Jaime Gallardo-Alvarado and Juan-de-Dios Posadas-Garcia:
**Mobility analysis and kinematics of the semi-general 2(3-RPS) series-parallel manipulator**.*Robotics and Computer-Integrated Manufactoring*29(6): 463-472, 2013. - Jaime Gallardo-Alvarado, Mohammad H. Abedinnasab, and Daniel Lichtblau:
**Simplified Kinematics for a Parallel Manipulator Generator of the Schoenflies Motion**.*Journal of Mechanisms and Robotics*8(6):061020-061020-10, 2016. - Bertrand Haas:
**A Simple Counterexample to Kouchnirenko’s Conjecture**.*Beitraege zur Algebra und Geometrie/Contributions to Algebra and Geometry*43(1):1-8, 2002. - Adlane Habed and Boubakeur Boufama:
**Camera self-calibration from bivariate polynomial equations and the coplanarity constraint**.*Image and Vision Computing*24(5):498-514, 2006. - Marshall Hampton and Richard Moeckel:
**Finiteness of stationary configurations of the four-vortex problem**.*Transactions of the American Mathematical Society*361(3): 1317-1332, 2009. - Jonathan Hauenstein, Jose Israel Rodriguez, and Bernd Sturmfels:
**Maximum Likelihood for Matrices with Rank Constraints**.*Journal of Algebraic Statistics*5(1): 18-38, 2014. - Christoph Hellings, David A. Schmidt, and Wolfgang Utschick:
**Optimized beamforming for the two stream MIMO interference channel at high SNR**. In 2009 Internatial ITG Workshop on Smart Antennas (WSA 2009), February 16-19, Berlin, Germany, pages 88-95. - Gabor Horvath:
**Moment Matching-Based Distribution Fitting with Generalized Hyper-Erlang Distributions**. In*Analytical and Stochastic Modeling Techniques and Applications*, Lecture Notes in Computer Science, Volume 7984, pages 232-246, 2013. - X.G. Huang:
**Forward Kinematics for a Parallel Platform Robot**.*Communications in Computer and Information Sciences*86:529-532, 2011. - Xiguang Huang, Qizheng Liao, Shimin Wei, and Qiang Xu:
**Five precision point-path synthesis of planar four-bar linkage using algebraic method**.*Frontiers of Electrical and Electronic Engineering in China*3(4):470-474, 2008. - Xiguang Huang, Qizheng Liao, Shimin Wei, Qiang Xu, and Shuguang Huang:
**The 4SPS-2CCS generalized Stewart-Gough Platform mechanisms and its direct kinematics**. In*Proceedings of the 2007 IEEE International Conference on Mechatronics and Automation*, August 5-8, 2007, Harbin, China. Pages 2472-2477, 2007. - Hamadi Jamali, Tokunbo Ogunfunmi:
**Stationary points of the finite length constant modulus optimization**.*Signal Processing*82(4): 625-641, 2002. - Hamadi Jamali:
**The unsupervised optimum linear finite length filter for fourth order wide sense stationary single output systems**.*Digital Signal Processing*, in press, 2018. - A. Jensen, A. Leykin, and J. Yu:
**Computing tropical curves via homotopy continuation**.*Experimental Mathematics*25(1): 83–93, 2016. - Libin Jiao, Bo Dong, Jintao Zhang, and Bo Yu:
**Polynomial Homotopy Methods for the Sparse Interpolation Problem Part I: Equally Spaced Sampling**.*SIAM J. Numer. Anal.*54(1): 462-480, 2016. - Bjorn Johansson, Magnus Oskarsson, and Kalle Astrom:
**Structure and motion estimation from complex features in three views**. In the Online ICVGIP-2002 Proceedings (Indian Conference on Computer Vision, Graphics and Image Processing). - M. Kara-Zaitri, D. Arzelier, and C. Louembet:
**Mixed iterative algorithm for solving optimal implusive time-fixed rendezvous problem**.*American Institute of Aeronautics and Astronautics Guidance, Navigation, and Control Conference*, Toronto, Canada, 02-05 August 2010. - Yoni Kasten, Meirav Galun, Ronen Basri:
**Resultant Based Incremental Recovery of Camera Pose from Pairwise Matches**.*2019 IEEE Winter Conference on Applications of Computer Vision (WACV)*, Waikoloa Village, HI, USA, 7-11 January 2019, pages 1080-1088, IEEE 2019. - Dimitra Kosta and Kaie Kubjas:
**Maximum Likelihood Estimation of Symmetric Group-Based Models via Numerical Algebraic Geometry**.*Bulletin of Mathematical Biology*, October 2018, pages 1-24. - P.U. Lamalle, A. Messiaen, P. Dumortier, F. Durodie, M. Evrard, F. Louche:
**Study of mutual coupling effects in the antenna array of the ICRH plug-in for ITER**.*Fusion Engineering and Design*74:359-365, 2005. - E. Lee and C. Mavroidis:
**Solving the Geometric Design Problem of Spatial 3R Robot Manipulators Using Polynomial Continuation**.*Journal of Mechanical Design, Transactions of the ASME*124(4):652-661, 2002. - E. Lee and C. Mavroidis:
**Four Precision Points Geometric Design of Spatial 3R Manipulators**. In the*Proceedings of the 11th World Congress in Mechanism and Machine Sciences*, August 18-21, 2003, Tianjin, China. China Machinery Press, edited by Tian Huang. - E. Lee and C. Mavroidis:
**Geometric Design of 3R Manipulators for Reaching Four End-Effector Spatial Poses**.*International Journal for Robotics Research*, 23(3):247-254, 2004. - E. Lee, C. Mavroidis, and J. Morman:
**Geometric Design of Spatial 3R Manipulators**. In*Proceedings of the 2002 NSF Design, Service, and Manufacturing Grantees and Research Conference*, San Juan, Puerto Rico, January 7-10, 2002. - Dimitri Leggas and Oleg V. Tsodikov:
**Determination of small crystal structures from a minimum set of diffraction intensities by homotopy continuation**.*Acta Crystallographica Section A*71(3): 319-324, 2015. - Dawei Leng and Weidong Sun:
**Finding All the Solutions of PnP Problem**. In*IST 2009 - International Workshop on Imaging Systems and Techniques*, Shenzhen, China, May 11-12, 2009. Pages 348-352, IEEE, 2009. - Anton Leykin:
**Numerical Primary Decomposition**. In*Proceedings of ISSAC 2008*, edited by David Jeffrey, pages 165-164, ACM 2008. - Anton Leykin and Frank Sottile:
**Computing Monodromy via Parallel Homotopy Continuation**. In*Proceedings of the 2007 International Workshop on Parallel Symbolic Computation (PASCO‘07)*, pages 97-98, ACM 2007. (on CDROM) - Anton Leykin and Frank Sottile:
**Galois groups of Schubert problems via homotopy computation**.*Mathematics of Computation*78: 1749-1765, 2009. - Shaobai Li, Srinandan Dasmahapatra, and Koushik Maharatna:
**Dynamical System Approach for Edge Detection Using Coupled FitzHugh-Naguma Neurons**.*IEEE Transactions on Image Processing*24(12), 5206-5219, 2015. - Ross A. Lippert:
**Fixing multiple eigenvalues by a minimal perturbation**.*Linear Algebra Appl.*432(7): 1785-1817, 2010. - Abdrhaman Mahmoud, Bo Yu, Xuping Zhang:
**Solving Variable-Coefficient Fourth-Order ODEs with Polynomial Nonlinearity by Symmetric Homotopy Method**.*Applied and Computational Mathematics*7(2): 58-70, 2018. - M. Maniatis and O. Nachtmann:
**Stability and symmetry breaking in the general three-Higgs-double model**.*Journal of High Energy Physics*2015:58, February 2015. - F. Meng, J. W. Banks, W. D. Henshaw, and D. W. Schwendeman:
**A stable and accurate partitioned algorithm for conjugate heat transfer.***Journal of Computational Physics*344: 51-85, 2017. - Hyosang Moon and Nina P. Robson:
**Design of spatial non-anthropomorphic articulated systems based on arm joint constraint kinematic data for human interactive robotics applications**. DETC2015-46530. In the*Proceedings of the ASME 2015 International Design Engineering Technical Conferences & Computers and Information in Engineering Conference*. IDETC/CIE 2015. August 2-5, 2015, Boston Massachusetts. - Marc Moreno Maza, Greg Reid, Robin Scott, and Wenyuan Wu:
**On Approximate Triangular Decompositions I. Dimension Zero**. In the*SNC 2005 Proceedings*. International Workshop on Symbolic-Numeric Computation. Xi’an, China, July 19-21, 2005. Edited by Dongming Wang and Lihong Zhi. Pages 250-275, 2005. - Andrew J. Newell:
**Transition to supermagnetism in chains of magnetosome crystals**.*Geochemistry Geophysics Geosystems*10(11):1-19, 2009. - Girijanandan Nucha, Georges-Pierre Bonneau, Stefanie Hahmann,
and Vijay Natarajan.
**Computing Contour Trees for 2D piecewise Polynomial Functions**. In*Eurographics Conference on Visualization (EuroVis)*2017, edited by J. Heer, T. Ropinski, and J. van Wijk, pages 24-33, Computer Graphics Forum, Wiley & Sons Ltd., 2017. - Nida Obatake, Anne Shiu, Xiaoxian Tang, and Angelica Torres:
**Oscillations and bistability in a model of ERK regulation**. arXiv:1903.02617 - M. Oskarsson, A. Zisserman and K. Astrom:
**Minimal Projective Reconstruction for combinations of Points and Lines in Three Views**. In the*Electronic Proceedings of BMVC2002 - The 13th British Machine Vision Conference 2002*, pages 63 - 72. - P.A. Parrilo and B. Sturmfels.
**Minimizing polynomial functions**. In S. Basu and L. Gonzalez-Vega, editors,*Algorithmic and quantitative real algebraic geometry*, volume 60 of*DIMACS Series in Discrete Mathematics and Theoretical Computer Science*, pages 83-99. AMS, 2003. - Alba Perez and J.M. McCarthy:
**Dual Quaternion Synthesis of Constrained Robotic Systems**.*Journal of Mechanical Design*126(3): 425-435, 2004. - Nina Patarinsky-Robson, J. Michael McCarthy, and Irem Y. Tumer:
**The algebraic synthesis of a spatial TS chain for a prescribed acceleration task**.*Mechanism and Machine Theory*43(10): 1268-1280, 2008. - Nina Patarinsky-Robson, J. Michael McCarthy, and Irem Y. Tumer:
**Failure Recovery Planning for an Arm Mounted on an Exploratory Rover**.*IEEE Transactions on Robotics*25(6):1448-1453, 2009. - Jose Israel Rodriguez:
**Combinatorial excess intersection**.*Journal of Symbolic Computation*68(2): 297-307, 2015. - Roger E. Sanchez-Alonso, Jose-Joel Gonzalez-Barbosa, Eduardo
Castilo-Castaneda, and Jaime Gallardo-Alvarado:
**Kinematic analysis of a novel 2(3-RUS) parallel manipulator**.*Robotica*, available on CJO2015. - H. Schreiber, K. Meer, and B.J. Schmitt:
**Dimensional synthesis of planar Stephenson mechanisms for motion generation using circlepoint search and homotopy methods**.*Mechanism and Machine Theory*37(7):717-737, 2002. - Ben Shirt-Ediss, Ricard V. Sole, and Kepa Ruiz-Mirazo:
**Emergent Chemical Behavior in Variable-Volume Protocells**.*Life*5: 181-121, 2015. - Hythem Sidky, Jonathan K. Whitmer, and Dhagash Mehta:
**Reliable mixture critical point computation using polynomial homotopy continuation**.*AIChE Journal. Thermodynamics and Molecular-Scale Phenomena*, 2016. doi:10.1002/aic.15319 - Frank Sottile:
**Real Schubert Calculus: Polynomial systems and a conjecture of Shapiro and Shapiro**.*Experimental Mathematics*9(2): 161-182, 2000. - H. Stewenius and K. Astrom:
**Structure and Motion Problems for Multiple Rigidly Moving Cameras**. In*Computer Vision - ECCV 2004: 8th European Conference on Computer Vision, Prague, Czech Republic, May 11-14, 2004. Proceedings, Part III*. Edited by T. Pajdla and J. Matas. Lecture Notes in Computer Science 3023, pages 252-263, Springer, 2004. - H.-J. Su and J.M. McCarthy:
**Kinematic Synthesis of RPS Serial Chains**. In the*Proceedings of the ASME Design Engineering Technical Conferences*(CDROM). Paper DETC03/DAC-48813. Chicago, IL, Sept. 02-06, 2003. - H.-J. Su and J.M. McCarthy:
**Synthesis of Compliant Mechanisms with Specified Equilibrium Positions**. In the*Proceedings of the ASME International Design Engineering Technical Conferences*. Paper DETC 2005-85085. Long Beach, CA, Sept. 24-28 2005. - H.-J. Su and J.M. McCarthy:
**Kinematic Synthesis of RPS Serial Chains for a Given Set of Task Positions**.*Mechanism and Machine Theory*40(7):757-775, 2005 - H.-J. Su and J.M. McCarthy:
**A Polynomial Homotopy Formulation of the Inverse Static Analysis of Planar Compliant Mechanisms**.*ASME Journal of Mechanical Design*128(4): 776-786, 2006. - H.-J. Su, C.W. Wampler, and J.M. McCarthy:
**Geometric Design of Cylindric PRS Serial Chains**.*ASME Design Engineering Technical Conferences*, Chicago, IL, Sep 2-6, 2003. - Weronika J. Swiechowicz and Yuanfang Xiang:
**Numerical Methods for Estimating Correlation Coefficient of Trivariate Gaussians**(sponsor: Sonja Petrovic) in Volume 8 of*SIAM Undergraduate Research Online (SIURO)*, 2015. - Attila Tanács and Joakim Lindblad and Nataša Sladoje and Zoltan Ka:
**Estimation of linear deformations of 2D and 3D fuzzy objects**.*Pattern Recognition*48(4):1391-1403, 2015. - N. Trawny, X.S. Zhou, K.X. Zhou, S.I. Roumeliotis:
**3D Relative Pose Estimation from Distance-Only Measurements**. In the*Proceedings of the 2007/IEEE/RSJ International Conference on intelligent Robots and Systems*. San Diego, CA, Oct 29-Nov 2, 2007, pages 1071-1078, IEEE, 2007. - T. Turocy:
**Towards a black-box solver for finite games: Computing all equilibria with Gambit and PHCpack**. In*Software for Algebraic Geometry*, volume 148 of the IMA volumes in Mathematics and its Applications, edited by M.E. Stillman, N. Takayama, and J. Verschelde, pages 133-148, Springer-Verlag, 2008. - Konstantin Usevich and Ivan Markovsky:
**Structured low-rank approximation as a rational function minimization**. In 16th IFAC Symposium on System Identification Brussels, 11-13 Jul 2012, pages 722-727. - J. Vanderstukken, A. Stegeman, and L. De Lathauwer:
**Systems of polynomial equations, higher-order tensor decompositions and multidimensional harmonic retrieval: A unifying framework. Part I: The canonical polyadic decomposition.**Available as ftp://ftp.esat.kuleuven.be/pub/stadius/nvervliet/vanderstukken2017systems1.pdf - A.D. Viquerat:
**A continuation-based method for finding laminated composite stacking sequences.***Composite Structures*238 (2020) 111872. https://doi.org/10.1016/j.compstruct.2020.111872 - C.W. Wampler:
**Isotropic coordinates, circularity and Bezout numbers: planar kinematics from a new perspective**. In the*Proceedings of the 1996 ASME Design Engineering Technical Conference*. Irvine, CA, Aug 18-22, 1996. Available on CD-ROM. - Wenyuan Wu and Greg Reid:
**Symbolic-numeric computation of implicit Riquier bases for PDE**. In the*Proceedings of the 2007 International Symposium on Symbolic and Algebraic Computation*, edited by C.W. Brown, pages 377-385, ACM 2007. - Wenyuan Wu and Zhonggang Zeng:
**The Numerical Factorization of Polynomials.***Foundations of Computational Mathematics*17(1): 259-286, 2017. - Jonathan Widger and Daniel Grosu:
**Parallel Computation of Nash Equilibria in N-Player Games**. In the*Proceedings of the 12th IEEE International Conference on Computational Science and Engineering (CSE 2009)*, August 29-31, 2009, Vancouver, Canada, pages 209-215. - F. Xie, G. Reid, and S. Valluri:
**A numerical method for the one dimensional action functional for FBG structures**.*Can J. Phys.*76: 1-21, 2002. - Hong Bing Xin, Qiang Huang, and Yueqing Yu:
**Position and Orientation Analyses of Mechanism by PHCpack Solver of Homotopy Continuation**.*Applied Mechanics and Materials*152-254: 1779-1784, 2012. - Ke-hu Yang, Dan-ying Lu, Xiao-qing Kuang, and Wen-Shen Yu:
**Harmonic Elimination for Multilevel Converters with Unequal DC levels by Using the Polynomial Homotopy Continuation Algorithm**. In the Proceedings of the 35th Chinese Control Conference, July 27-29, 2016, Chengdu, China, pages 9969-9973, IEEE. - K. Yang and R. Orsi:
**Static output feedback pole placement via a trust region approach**.*IEEE Transactions on Automatic Control*52(11): 2146-2150, 2007. - Yan Yang, Yao Zhang, Fangxing Li, and Haoyong Chen:
**Computing All Nash Equilibria of Multiplayer Games in Electricity Markets by Solving Polynomial Equations**.*IEEE Transactions on Power Systems*27(1): 81-91, 2012. - Jun Zhang and Mohan Sarovar:
**Identification of open quantum systems from observable time traces**.*Physical Review A*91, 052121, 2015. - Shiqiang Zhang, Shufang Zhang, and Yan Wan:
**Biorthogonal Wavelet Construction Using Homotopy Method**.*Chinese Journal of Electronics*24(4), pages 772-775, 2015. - X. Zhang, J. Zhang, and B. Yu:
**Symmetric Homotopy Method for Discretized Elliptic Equations with Cubic and Quintic Nonlinearities.***Journal of Scientific Computing*70(3): 1316-1335, 2017. - Xun S. Zhou and Stergios I. Roumeliotis:
**Determining 3-D Relative Transformations for Any Combination of Range and Bearing Measurements.***IEEE Transactions on Robotics*29(2):458-474, 2013. - Lifeng Zhou, Hai-Jun Su, Alexander E. Marras, Chao-Min Huang,
Carlos E. Castro:
**Projection kinematic analysis of DNA origami mechanisms based on a two-dimensional TEM image.***Mechanisms and Machine Theory*109:22-38, 2017. - Lailai Zhu and Howard A. Stone:
**Harnessing elasticity to generate self-oscillation via an electrohydrodynamic instability.***J. Fluid Mech.*888, Article ID A31, 35 p., 2020.

In addition to the publications listed above, PHCpack was used as a benchmark to measure the progress of new algorithms in the following papers:

- Ali Baharev, Ferenc Domes, Arnold Neumaier:
**A robust approach for finding all well-separated solutions of sparse systems of nonlinear equations**.*Numerical Algorithms*76:163-189, 2017. - Ada Boralevi, Jasper van Doornmalen, Jan Draisma, Michiel E. Hochstenbach,
and Bor Plestenjak:
**Uniform Determinantal Representations**.*SIAM J. Appl. Algebra Geometry*, vol. 1, pages 415-441, 2017. - P. Breiding and S. Timme.
**HomotopyContinuation.jl: A package for homotopy continuation in Julia.**In J. H. Davenport, M. Kauers, G. Labahn, and J. Urban, editors,*Mathematical Software – ICMS 2018. 6th International Conference, South Bend, IN, USA, July 24-27, 2018. Proceedings*, volume 10931 of*Lecture Notes in Computer Science*, pages 458-465. Springer-Verlag, 2018. - Timothy Duff, Cvetelina Hill, Anders Jensen, Kisun Lee, Anton Leykin,
and Jeff Sommars:
**Solving polynomial systems via homotopy continuation and monodromy**.*IMA Journal of Numerical Analysis*. In Press, available online 13 April 2018. - T. Gao and T.Y. Li:
**Mixed volume computation via linear programming**.*Taiwanese Journal of Mathematics*4(4): 599-619, 2000. - T. Gao and T.Y. Li:
**Mixed volume computation for semi-mixed systems**.*Discrete Comput. Geom.*29(2):257-277, 2003. - L. Granvilliers:
**On the Combination of Interval Constraint Solvers**.*Reliable Computing*7(6): 467-483, 2001. - Jonathan D. Hauenstein, Andrew J. Sommese, and Charles W. Wampler:
**Regeneration Homotopies for Solving Systems of Polynomials***Mathematics of Computation*80(273): 345-377, 2011. - S. Kim and M. Kojima:
**Numerical Stability of Path Tracing in Polyhedral Homotopy Continuation Methods**.*Computing*73(4): 329-348, 2004. - Y. Lebbah, C. Michel, M. Rueher, D. Daney, and J.P. Merlet:
**Efficient and safe global constraints for handling numerical constraint systems**.*SIAM J. Numer. Anal.*42(5):2076-2097, 2005. - T.L. Lee, T.Y. Li, and C.H. Tsai:
**HOM4PS-2.0: a software package for solving polynomial systems by the polyhedral homotopy continuation method**.*Computing*83(2-3): 109-133, 2008. - Anton Leykin:
**Numerical Algebraic Geometry**.*The Journal of Software for Algebra and Geometry*volume 3, pages 5-10, 2011. - T.Y. Li and X. Li:
**Finding Mixed Cells in the Mixed Volume Computation**.*Foundations of Computational Mathematics*1(2): 161-181, 2001. - T.Y. Li, X. Wang, and M. Wu:
**Numerical Schubert Calculus by the Pieri Homotopy Algorithm**.*SIAM J. Numer Anal.*40(2): 578-600, 2002. - Bernard Mourrain, Simon Telen, and Marc Van Barel:
**Solving Polynomial Systems Efficiently and Accurately.**arXiv:1803.07974v2 [math.AG] 22 Mar 2018. - J.M. Porta, L. Ros, T. Creemers, and F. Thomas:
**Box approximations of planar linkage configuration spaces**.*Journal of Mechanical Design*129(4):397-405, 2007. - Laurent Sorber, Marc Van Barel, and Lieven De Lathauwer:
**Numerical solution of bivariate and polyanalytic polynomial systems**.*SIAM J. Numer. Anal.*52(4):1551-1572, 2014. - Yang Sun, Yu-Hui Tao, Feng-Shan Bai:
**Incomplete Groebner basis as a preconditioner for polynomial systems**.*Journal of Computational and Applied Mathematics*226(1):2-9, 2009. - Simon Telen and Marc Van Barel:
**A stabilized normal form algorithm for generic systems of polynomial equations**.*Journal of Computational and Applied Mathematics*342(November 2018): 119-132, 2018. - S. Telen, B. Mourrain, and M. Van Barel:
**Solving Polynomial Systems via a Stabilized Representation of Quotient Algebras.**arXiv:1711.04543v1 [math.AG] 13 Nov 2017 - S. Telen, B. Mourrain, and M. Van Barel:
**Solving Polynomial Systems via Truncated Normal Forms.***SIAM J. Matrix Anal. Appl.*39(3):1421-1447, 2018. - A. Zachariah and Z. Charles:
**Efficiently Finding All Power Flow Solutions to Tree Networks.**In*Fifty-Fifth Annual Allerton Conference. Allerton House, UIUC, Illinois, USA. October 3-6, 2017*, pages 1107-1114, IEEE, 2017.

PHCpack was used to develop new homotopy algorithms:

- Bo Dong, Bo Yu, and Yan Yu:
**A symmetric and hybrid polynomial system solving method for mixed trigonometric polynomial systems**.*Mathematics of Computation*83(288): 1847-1868, 2014. - Bo Yu and Bo Dong:
**A hybrid polynomial system solving method for mixed trigonometric polynomial systems**.*SIAM J. Numer. Anal.*46(3): 1503-1518, 2008. - Xuping Zhang, Jintao Zhang, and Bo Yu:
**Eigenfunction expansion method for multiple solutions of semilinear elliptic equations with polynomial nonlinearity***SIAM J. Numer. Anal.*51(5): 2680-2699, 2013.

Last, but certainly not least, there is the wonderful book of Bernd Sturmfels which contains a section on computing Nash equilibria with PHCpack.

- B. Sturmfels:
**Solving Systems of Polynomial Equations**. CBMS Regional Conference Series of the AMS, Number 97, 2002.

So we have to end quoting Bernd Sturmfels:
*polynomial systems are for everyone.*

## Acknowledgments¶

Since 2001, the code in PHCpack improved thanks to the contributions of many PhD students at the University of Illinois at Chicago. Their names, titles of PhD dissertation, and year of PhD are listed below:

- Yusong Wang:
*Computing Dynamic Output Feedback Laws with Pieri Homotopies on a Parallel Computer*, 2005. - Ailing Zhao:
*Newton’s Method with Deflation for Isolated Singularities of Polynomial Systems*, 2007. - Yan Zhuang:
*Parallel Implementation of Polyhedral Homotopy Methods*, 2007. - Kathy Piret:
*Computing Critical Points of Polynomial Systems using PHCpack and Python*, 2008. - Yun Guan:
*Numerical Homotopies for Algebraic Sets on a Parallel Computer*, 2010. - Genady Yoffe:
*Using Parallelism to compensate for Extended Precision in Path Tracking for Polynomial System Solving*, 2012. - Danko Adrovic:
*Solving Polynomial Systems with Tropical Methods*, 2012. - Xiangcheng Yu:
*Accelerating Polynomial Homotopy Continuation on Graphics Processing Units*, 2015. - Jeff Sommars:
*Algorithms and Implementations in Computational Algebraic Geometry*, 2018. - Nathan Bliss:
*Computing Series Expansions of Algebraic Space Curves*, 2018.

Anton Leykin contributed to the application of message passing
in a parallel implementation of monodromy to decompose an equidimensional
solution set into irreducible components.
The Maple interface `PHCmaple`

was written jointly with Anton Leykin.
The work of Anton Leykin also paved the way for the Macaulay2 interface,
which was further developed into `PHCpack.m2`

in joint work with
Elizabeth Gross and Sonja Petrovic.
The `PHCpack.m2`

(and also PHCpack itself) improved during various
Macaulay2 workshops, with the help of
Taylor Brysiewicz, Diego Cifuentes, Corey Harris, Kaie Kubjas,
Anne Seigal, and Jeff Sommars.

The software has been developed with GNAT GPL, the gnu-ada compiler.

This material is based upon work supported by the National Science Foundation under Grants No. 9804846, 0105739, 0134611, 0410036, 0713018, 1115777, 1440534, and 1854513. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.