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OpenMCTDHB User manual

1. 10 d0 amp RUNPARAMETERS ABSTIME 0 000000000000000 MAXTIME 100 000000000000000 TOLERROR 1 00000000000000022 007 RESTART T RELAX F READPOTENTIALST PROPDIRECTION 1 TAG BJJ potential 1d The file contains several namelists which we will now list SYSTEMPARAMETERS contains information about the interaction strength LAMBDAO the number of particles NPAR the number of orbitals MORB the number of dimen sions of the problem Dims and a variable USEIMEST to decide whether the IMEST algorithm is to be used T to evaluate interaction matrix elements or not F If MORB 1 the MCTDHB equations reduce to the Gross Pitaevskii equation which is then solved If MORB 2 the MCTDHB equations constitute the systematic many body general Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 10 Basic Usage ization of Gross Pitaevskii please see the literature for details Currently up to two orbitals can be used in OpenMCTDHB If USEIMEST F a delta function is used as an interaction potential actually just a square box of the width of one grid point A description of the IMEST algorithm can be found in Kaspar Sakmann s PhD thesis If USEIMEST T currently a gaussian interaction potential is used Other interaction potentials can be implemente dusing the IMEST algorithm as long as the value of the interaction potential depends on the distance between two points only IMESTPA
2. Functions must not have pointer results All dummy arguments except pointers must include the INTENT clause in their declaration Error conditions When an error condition occurs inside a function procedure a message describing what went wrong should be printed The name of the routine in which the error occurred must be included It is acceptable to terminate execution within a package but the developer may instead wish to return an error flag through the argument list Functions procedures that perform the same function but for different types sizes of arguments should be overloaded to minimize duplication and ease the maintainability When explicit interfaces are needed use modules or contain the subroutines in the calling programs through CONTAINS statement for simplicity Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 24 Developer Guidelines for OpenMCTDHB Guidelines Do not use external routines Subroutine not contained within a module and not within the CONTAINS statement of the main program as in some cases these functions need interface blocks that would need to be updated each time the interface of the external routine is changed An exception is made for the external routines that are passed to the integrators because they were written like that a long time ago 5 11 Inputs Outputs Standards I O statements on external files should cont
3. 3 2 2 tar gz b cd into src FFTW fftw 3 2 2 d e a b c Type configure prefix lt full path to the src FFTW directory gt d Type make this will take a while e Type make install You should now have a few more directories in src FFTW e g src FFTW include If this did not work for you start reading the README of FFTW or contact one of your system administrators Alternatively you can try one of the other installation options ii If you already have the FFTW library installed somewhere else and want to use it you will have to set the path to it in the makefile It should be the path to the directory that contains the include directory of the FFTW library cd into the src directory and type make This should compile the program and put the executable OpenMCTDHB x in the base directory If you would like to use the separate program v to create files containing external potentials cd into the create V ext file directory and type make This should compile the program and put the executable V_ext x in the directory above src INSTALLATION gfortran with ACML 4 4 Assuming you have the ACML library installed we used version 4 4 the installation proceeds as follows cd into the src directory open the file Makefile gfortran acml and set the path to the ACML library type echo LD LIBRARY PATH the path to your ACML library has to be in the list that will appear If it is not ad
4. ing conflicts Exception to previous statement is when a module is entirely dedi cated to PUBLIC data functions e g a module dedicated to constants Initialize all variables Do not assume machine default value assignments Currently the code is purely procedural and no derived data types are used Before using object oriented features contact all other developers Do not initialize variables of one type with values of another Do not use the operators and with floating point expressions as operands Check instead the departure of the difference from a pre defined nu merical accuracy threshold e g epsilon comparison Avoid to share data via use association Large arrays such as should be passed explicitly wherever possible The structure of the integrators makes this complicated at the moment but the general rule is that it has to be clear what happens and what variables are modified when calling a routine by reading through the main program Use explicit shape dummy arrays i e pass the sizes of all arrays to the subroutines Try to minimize use association of variables to maximize modularity of the code Guidelines In mixed mode expressions and assignments where variables of different types are mixed within an expression or in an assignment type conversions should be written explicitly not assumed Do not compare expressions of dif ferent types for instance Explicitly perf
5. orbs inp which contains the orbital s used to expand the wave function 4 restart coef inp which contains the coefficients of the wave function The orbital and the coefficient files can also be left out if a computation is to start from default orbitals gaussians see below Also the external potential can be defined within the program but this requires the recompilation of the program It is recommended to use this option only for time dependent external potentials 3 2 1 The file runpars inp We begin with a discussion of the runpars inp file of the BJJ propagation 1d example Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 3 2 Input files 9 amp SYSTEMPARAMETERS LAMBDAO 1 53535353535353531E 003 NPAR 100 MORB 2 DIMS 15 USEIMEST F amp IMESTPARAMETERS IMESTPARAMETER1 5 00000000000000028bE 002 amp GRIDPARAMETERS Xl 12 000000000000000 XF 12 000000000000000 Yl 0 0000000000000000 YF 0 0000000000000000 Zl 0 0000000000000000 ZF 0 0000000000000000 NDX 251 NDY 15 NDZ 5 5 v amp PRINTPARAMETERS TINYSTEP 0 10000000000000001 PRINTSTEP 5 0000000000000000 PRINTALLSTEP 70 331964898799995 PRINTCORRELATIONFUNCS 0 REALSPACE2D FALSE MOMSPACE2D FALSE x1slice 0 d0 x2slice 0 d0 yislice 0 d0 y2slice 0 d0 x1const TRUE ylconst TRUE x2const FALSE y2const FALSE Pnot FALSE xstart 10 d0 xstop
6. should give you two files containing the potential called V_extHarmonic 2d 64x64 inp and V extHarmonic 2d 64x64 nml which contains the parameters you just entered Here is a listing of a file that generates a 2D harmonic trap located at the origin with unit trap frequencies in x and y amp GENERALPARS 6 0000000000000000 XF 6 0000000000000000 Yl 6 0000000000000000 YF 6 0000000000000000 Zl 0 0000000000000000 Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 3 3 How to setup a new problem 13 ZF 0 0000000000000000 NDX 64 NDY 64 NDZ fs DIMS 25 amp TAGNAME TAG Harmonic 2d 64x64 amp POTENTIALNAME POTNAME HARMONIC amp HARMONICPARAMETERS X0 0 0000000000000000 YO 0 0000000000000000 20 0 0000000000000000 W X 1 00000000000000000 W_Y 1 00000000000000000 W_Z 1 00000000000000000 gt 7 You can now copy the file with the external potential into any run directory and use it When you do so make sure to rename it to V_ext inp because that s what the propram will look for If you choose POTNAME BJJ you will get a bosonic Josephson Junction potential Feel free to add other external potentials 3 3 2 Relaxation starting from the default initial guess wave function In the previous subsection you have generated a 2D external harmonic potential You can now use this potential together with a runpars inp file to relax the system
7. write or read followed by an underscore and a variable e g get liebLinigerParameter Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 20 Developer Guidelines for OpenMCTDHB Each function subroutine has to contain a Doxygen friendly header explain ing the purpose the author and the date when it was first introduced into the code When modifying existing code the name of the modifying developer should be added to the list of authors together with the modification made Preprocessor macros should be used on the lowest level only to allow for dif ferent libraries to be used e g for calls to different FFT libraries in modulefft F90 Do not use GOTO statements These are hard to maintain and complicate understanding the code Remove code that was used for debugging once this is complete Always use the notation even if there are no attributes Line up vertically attributes variables comments within the variables decla ration section Remove unused variables and unused code Guidelines Use construct names to name loops to increase readability especially in nested loops Similarly use construct names in subroutines functions main programs mod ules operator interface etc Include comments to describe the input output and local variables of all pro cedures Use comments as required to delineate significant functional sections of co
8. Portability Inter systems Compatibility Standards Source code shall conform to the ISO Fortran95 standard No compiler or platform dependent extensions shall be used e While use of IOSTAT and STAT is encouraged to handle I O and other status errors no interpretation of actual returned values shall be made as these values are compiler dependent Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 5 5 Readability Maintainability 19 Guidelines Note that STOP is a F90 95 standard EXIT N is an extension and should be avoided It is recognized that STOP does not necessarily return an error code If an error code must be passed to a script for instance then the extension EXIT could be used but within a central place so that to limit its occurrences within the code to a single place Precision Parameterizations should not rely on vendor supplied flags to sup ply a default floating point precision or integer size The F90 95 KIND feature should be used instead Do not use tab characters in the code to ensure it will look as intended when ported They are not part of the Fortran characters set Recommendations For applications requiring interaction with independently developed frameworks the use of KIND type for all variables declaration is encouraged to facilitate the integration 5 5 Readability Maintainability Standards Use free format syntax All
9. body density Pro 777 p x dx xstart p xstart xstop are real values which determine the evaluation of the nonescape prob ability RUNPARAMETERS determines the several parameters for this particular run ABSTIME the initial time MAXTIME the maximal time TOLERROR the maximal error allowed in each step of the propagation This is given as a parameter to the integrators for the coefficients and the oribitals RESTART can be T or F if true the files restart orbs inp and restart coef inp are read in otherwise the computation will start from some default orbitals which can be useful for relaxation computations RELAX can be T or F if T the system is propagated in imaginary time in order to reach the ground state if PROPDIRECTION 1 Otherwise propagated in real time READPOTENTIAL can be T or F if T the program will read the potential from the input file V_ext inp if F the external potential defined in the subroutine get V ext will be used This latter option also allows to use time dependent external potentials PROPDIRECTION can be 1 or 1 if 1 and RELAX F the Schr dinger equation is prop agated forward in time if 1 and RELAX F the Schr dinger equation is propagated backward in time TAG is a user defined string that will be attached to all output files Allows to give computations meaningful names 3 2 2 The file V ext inp The file V extinp contains the external potential that is used in the computation I
10. current code Use of allocatable arrays is preferred to using pointers when possible To minimize risks of memory leaks and heap fragmentation Use of pointers is allowed when declaring an array in a subroutine and making it available to a calling program Always initialize pointer variables in their declaration statement using the NULL intrinsinc INTEGER POINTER x gt NULL Guidelines Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 5 9 Loops 23 Always deallocate allocated pointers and arrays This is especially important inside subroutines and inside loops Always test the success of a dynamic memory allocation and deallocation Recommendations Use of dynamic memory allocation is encouraged when sensible e g for input dependent variables It makes code generic and avoids declaring with maximum dimensions For simplicity use Automatic arrays in subroutines whenever possible instead of allocatable arrays 5 9 Loops Standards Do not use GO TO to exit cycle loops use instead EXIT or CYCLE state ments Do not number DO loops DO 10 10 CONTINUE instead name long loops etc eg readif IF THEN 5 10 Functions Procedures Standards Use the save declaration where appropriate Do not assume the value of the variable will be kept by the processor Do not use an entry in a function subprogram
11. new code must be written in free format Fortran 95 and all new files must have the F90 extension which means that they will also be preprocessed Use consistent indentation across the code Indent everything by two spaces See the file OpenMCTDHB F90 as a reference Also the comments should be indented this way this still needs some work Use the Fortran 90 to comment something Never use the old C Comments that are to enter the Doxygen documentation must start with either l gt for subroutine documentation or if dummy variables are documented inline See e g the module modulegrid F90 IMPORTANT Doxygen is case sensitive This means that you will have to make sure that all variables and subroutines that you write must always be written the same way Otherwise you will mess up the Doxygen documentation This is particularly important for subroutines Check this before you commit Use modules to organize source code Only one module per file Modules must have the same lower case only name as the file that they are in and start with with the word module All subroutines must be in modules Use meaningful understandable words for variables and parameters Do not abbreviate these words and concatenate words to camelCase notation first word lower case all following start with an upper case letter e g printLiebLiniger Subroutines should start with a verb preferably one of get
12. that the Hamiltonian of the problem is time independent Let s say you would like to study the many body ground state in a harmonic trap in 1 dimension In particular you would like to know whether the ground state of 100 bosons interacting via a delta function potential at a given interaction strength is of the Gross Pitaevskii type or not 3 3 1 Get the external potential The first thing you will have to do is to create a file containing the harmonic potential called v extinp You can either generate this file yourself e g using MatLab or you can use the little program V_ext x for this purpose Currently this program allows you to generate V_ext inp files only for two types of poten tials a 1D bosonic Josephson Junction potential and parametrized harmonic potentials in 1D 2D and 3D However it is not difficult to extend it to other potentials You will have to edit the files src mod module_create_V_ext F90 and src create_V_ext V_ext F90 for this purpose However to generate a 2D harmonic potential you only have to do the following 1 cd into the directory input HarmonicTrap 1D and open the file v ext nml 2 In this file you can specify the number of grid points the boundaries of the grid the zero of the potential and the trap frequencies in each direction You can give the potential a meaningful name here e g Harmonic 2d 64x64 3 copy or create a sym link to V ext x in the current directory and type V_ext x This
13. 2D determines whether the output of cuts through the one body and two body correlation functions in real space for 2 dimensional calculations is ac tivated MOMSPACE 2D determines whether the output of cuts through the one body and two body correlation functions in momentum space for 2 dimensional calculations is activated x1slice y1slice x2slice y2slice determine at which values the cuts of the correlation functions g 7 ri g xlLslice y1slice x2slice y2slice T or g 7 71 75 Poli ro g 74 75 gO xlstice ylslice x2slice y2slice are written for 2D computations Note that only two of these variables are adressed see ex planation for xtconst etc Depending on the value of MOMSPACE2D and REALSPACE2D the variables xtslice y1slice x2slice y2slice are interpreted as momenta or positions x1const y1const x2const y2const If MOMSPACE2D and or REALSPACE2D is true then exactly two of these variables have to be true too These two variables then determine which cuts are taken e g x1const TRUE y1const TRUE x1slice 0 d0 y1slice 0 d0 will write the correlations 1 0 d0 0 d0 x2 y2 7 and g 0 40 0 40 x2 y2 Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 3 2 Input files 11 Pnot is a logical variable which determines whether to write the nonescape prob ability for 1D calculations or not It is defined as an integral on the diagonal of the reduced one
14. 5 13 Repository etiquette 25 5 13 Repository etiquette Standards Before submitting make a test directory and run OpenMCTDHB using the inputs of the examples directory Then check whether you get the same results Please do not alter or add any files in exisiting examples directories They are intended for reference only Please take the time to document your commits sufficiently Remember that other people really have no idea about what you have been doing Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen
15. OpenMCTDHB User manual v2 3 written by Kaspar Sakmann and Axel Lode Nov 29 2012 Contents 1 Main Page 2 Installation 21 SYSTEMREQUIBEMENTS i 2222199 ox 303 09333 3 2 2 INSTALLATION gfortran with FFTW 4 2 3 INSTALLATION gfortran with ACML4 4 2 4 INSTALLATION pgf95 with ACML 3 Basic Usage v dy NQEKIIDW uos son Ae ee Rk ECE ee aS ac IMPIES 2 22 54 deae eem y SOY 9 A WS ae AS Seal DT mipasibp o Lomo oo ku ok eoe Rakha RE ons 32 2 2 oo omm mo eee Rom Rom 42 3 The file restat BSD s ne som modo Roe om mom Rm ER 3 24 The file restart coef inp 3 3 How to setup a new problem 3 3 1 3 3 2 Relaxation starting from the default initial guess wave function 4 Scripts 4 1 Scripts for any number of dimensions 4 A2 Scripts for 1d 4 3 Scripts for 2d computations e s sx 5 Developer Guidelines for OpenMCTDHB 5 1 Introductions sssri 44 25 4 ke ee teray eee 5 2 Encouraged Compilation 5 3 Encouraged Features 22s zs Rx is 5 4 Portability Inter systems Compatibility 5 5 Readability Maintainability gt lcs 5 6 MODUSIFIBES nodo 5744 bb aed ae ewe E Roe Po od bad
16. RAMETERS is a container for parameters in case the IMEST algorithm is used Currently IMESTPARAMETERt1 determines the width of a gaussian interac tion that is normalized such that for vanishing width the delta function potential is recovered GRIDPARAMETERS contains the parameters that determine the lower and upper box boundaries and the number of grid points in each direction PRINTPARAMETERS controls the frequency when certain files are printed TINYSTEP is the time step at which quantities are printed that are to be monitored as continous functions of time e g the natural orbital occupation numbers the energy of the syste in 1Dsystems the Lieb Liniger parameter and the density in the left half of space PRINTSTEP determines how frequently the density of the system and its momen tum distribution are plotted Additionally the files restart coef out and restart orbs out are printed out which can be used as new restart coef inp and restart orbs inp files in case a computation was interrupted or finished early These files are overwritten after every PRINTSTEP time units PRINTALLSTEP determines how frequently the coefficients and the orbitals are writ ten into files that are kept as well as the computation of correlation functions in case PRINTCORRELATIONS 1 PRINTCORRELATIONS determines whether correlation functions are to be computed Currently this works only for one dimensional problems Possible values 0 1 REALSPACE
17. ain the status specifier parameters errz end iostat as appropriate Recommendations e Use write rather than print statements for non terminal I O Use Character parameters or explicit format specifiers inside the Read or Write statement DO not use labeled format statements outdated 5 12 Fortran Features that are obsolescent and or discouraged Standards No Common blocks Modules are a better way to declare store static data with the added ability to mix data of various types and to limit access to contained variables through use of the ONLY and PRIVATE clauses No GO TOs use the CASE construct instead No arithmetic IF statements use the block IF construct instead No implicit changing of the shape of an array when passing it into a subrou tine Use the RESHAPE intrinsic Although actually forbidden in the standard it was very common practice in FORTRAN 77 to pass n dimensional arrays into a subroutine where they would say be treated as a 1 dimensional array This prac tice though banned in Fortran 90 is still possible with external routines for which no Interface block has been supplied This only works because of assumptions made about how the data is stored Guidelines Do not make use of the equivalence statement especially for variables of different types Use pointers or derived types instead Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen
18. an be found atthe OpenMCTDHB website OpenMCTDHB uses some of the libraries of the Hei delberg MCTDH package and comes with a copy of the FFTW library please see the links below If you use OpenMCTDHB or some results obtained from it in any publication we politely request that you cite 1 below You may also wish to cite the original MCTDHB paper 2 or the MCTDHB package 3 References 1 OpenMCTDHB v2 3 Sakmann Axel U J Lode A Streltsov O E Alon L S Cederbaum 2012 http OpenMCTDHB uni hd de 2 O E Alon A Streltsov L S Cederbaum Phys Rev A 77 033613 2008 3 The MCTDHB Package A Streltsov K Sakmann A U J Lode E Alon and L S Cederbaum Version 2 0 Heidelberg 2010 http MCTDHB uni hd de 2 Main Page Useful links The OpenMCTDHB website downloads manual developer guidelines roadmap etc The MCTDHB website The MCTDH website e FETW library Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen Chapter 2 Installation This file describes the Installation of OpenMCTDHB Start by downloading the package from here OpenMCTDHBv2 1 tar gz unpack it type tar xvzf OpenMCTDHBv2 1 tar gz and cd into the OpenMCTDHBv2 1 direc tory In the following all paths will be relative to this base directory This User Manual can be found in the doc directory The source code is documented using doxygen If you have doxyge
19. d and ANayS luos lon mo x o xke i e Re OEC SIE XOU ee Dos 5 8 Dynamic Memory Allocation Pointers np LBS uc Rm kane cR a ae hal Ges ed 5 10 FunctionsiProcedures lcs mmm ee mom 3 5 11 1 lt 5 5 12 Fortran Features that are obsolescent and or discouraged 5 13 15 15 15 16 Chapter 1 Main Page OpenMCTDHB is an open source package for the many body dynamics of ultracold bosons 1 It is an implementation of the MCTDHB algorithm 2 to solve the many body Schr dinger equation for bosons The OpenMCTDHB project was initiated by Kaspar Sakmann OpenMCTDHB can solve the many boson Schr dinger equation for 1D 2D and 3D problems at variable degree of accuracy The current version supports up to two orbitals and thereby allows to assess the validity of any Gross Pitaevskii computation on the many body level The code is portable serial and can be compiled using open source software only A number of scripts that come with the code allow to analyze the physics of a computation without the need to get deeply involved The goal of OpenMCTDHB is to make many boson dynamics accessible to everyone People 02007 2012 Kaspar Sakmann head of project Axel Lode Alexej Streltsov Ofir Alon Lorenz Cederbaum A user manual with worked through examples and installation instructions c
20. d it e g by typing export LD LIBRARY PATH path to your gfortran acml library type make f Makefile gfortran acml This should compile the program and put the executable OpenMCTDHB x in the base directory Proceed with step 3 of the previous installation instructions Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 2 4 INSTALLATION pgf95 with ACML 5 2 4 INSTALLATION pgf95 with ACML Assuming you have the PGI compiler pgf95 installed we used the 64 bit version 8 0 1 the installation proceeds as follows The compiler comes with its own copy of ACML and knows where to find it 1 type make f Makefile gfortran pgf95 This should compile the program and put the executable OpenMCTDHB x in the base directory 2 Proceed with step 3 of the previous installation instructions Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen Installation Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen Chapter 3 Basic Usage This Chapter discusses the basic usage of OpenMCTDHB It is assumed that you have successfully compiled OpenMCTDHB and that there is an executable OpenMCTDHB x in the base directory 3 1 Typical workflow We will now discuss the typical workflow using OpenMCTDHB OpenMCTDHB is de signed such that you should only have to compile it once and never again unless you intend to study particular problems with time dependent Hamiltonians The typical workflow i
21. de Do not use FORTRAN statements and intrinsinc function names as symbolic names Use named parameters instead of mmagic numbers REAL PARAMETER Pl 3 14159 Recommendations When writing new code adhere to the style standards of the existing code to keep consistency Use the same indentation for comments as for the rest of the code Functions procedures data that are naturally linked should be grouped in mod ules Limit to 80 the number of characters per line maximum allowed under ISO is 132 Use of operators lt gt lt gt is encouraged for readability instead of It gt le ge eq ne Use blanks to improve the appearance of the code to separate syntactic elements on either side of equal signs etc in type declaration statements Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 5 6 Robustness 21 5 6 Robustness Standards Use IMPLICIT NONE in all codes main programs modules etc To ensure correct size and type declarations of variables arrays All subroutines and functions MUST be in modules Write subroutines instead of copying code even if it appears just twice Also put even few lines of code that do something specific into a subroutine with a suitable name Use PRIVATE in modules before explicitly listing data functions procedures to be PUBLIC This ensures encapsulation of modules and avoids potential nam
22. intstep in the file runpars inp type scripts 1d plotprobabilityleft sh to plot the probability density in the left potential well as a function of time the temporal resolution is determined by the variable tinyStep in the runpars inp file type scripts plotnatoccs sh to see the natural orbital occupation numbers as a func tion of time type scripts 1d k density sh 100 to plot the one body momentum distribution at dif ferent time points The value 100 determines the largest value on the y axis of the plot These four scripts should give you an idea of what the physical system is doing The computation will finish after 100 time units The system has then tunneled through the barrier once You can now compare your result files to those given in the directory examples BJJ propagation 1d e g by typing vimdiff file examples BJJ propagation 1d lt file gt There should not be any significant difference between the results somewhere in the last few digits maybe You can try out any of the other 1d scripts in the scripts directory on this problem See the scripts chapter of this manual for details 3 2 Input files Usually it is necessary to provide the following input files to a computation We will illustrate this using the example we have just discussed in the previous section 1 runpars inp which contains parameters of the current run N V_ext inp which contains the external potential 3 restart
23. n any new code These features are known to be error prone difficult to maintain read or listed as obsolescent in the Fortran95 standard In many cases newer Fortran95 constructs provide the same functionality in a more readable and robust fashion 5 2 Encouraged Compilation Practices To increase robustness it is recommended to compile the code with as many compilers as available to minimize the errors that may be missed by using a single compiler If available the use of the ISO compiler option International Standardization Organization is encouraged to ensure that no extension is used within the code All parts of the code should be compiled using the all warnings option The only exception are the files in the lib directory which are taken from MCTDH 5 3 Encouraged Features These usually help in the robustness of the code by checking interface compatibility for example and in the readability maintainability and portability They are reminded here Encapsulation Use of modules for procedures functions data Dynamic Memory allocation for optimal memory usage Derived types or structures which generally lead to stable interfaces optimal memory usage compactness etc Optional and keyword arguments in using routines Functions subroutines overloading capability however do not overload operators in OpenMCTDHB Intrinsinc functions bits arrays manipulations kinds definitions etc 5 4
24. n installed version 1 7 3 you can generate the source code documentation yourself by typing doxygen Doxyfile 1 7 3 when you are in the doc directory Alternatively you can browse through the source Code Documentation online at the OpenMCTDHB website 2 44 SYSTEM REQUIREMENTS Currently ODCenMCTDHB has been tested on Linux only These installation instructions are therefore for Linux It is assumed that you have a recent version of gcc installed we used gcc version 4 3 2 There are at least three different options to install OpenMCTDHB the fully open source option using gfortran of the gcc compiler suite together with BLAS LAPACK and FFTW The second option uses gfortran together with the ACML library The third option uses pgf95 together with the ACML library 2 2 INSTALLATION gfortran with FFTW i The default is to use gfortran as a compiler together with the libraries BLAS LAPACK and FFTW We used gfortran version 4 3 2 and FFTW version 3 2 2 A copy of the Installation FFTW library can be found in the src FFTW directory just in case you haven t got it on your machine already 1 i This step assumes you haven t got FFTW 3 2 2 installed and will install FFTW 2 3 into the directory src FFTW this is where the default makefile of OpenMCTDHB expects to find FFTW if you don t like that install FFTW anywhere else and adjust the path in the makefile a cd into src FFTW and unpack FFTW type tar xvzf fftw
25. orm the type conversion first No include files should be used Use modules instead with USE statements in calling programs Structures derived types should be defined within their own module Proce dures Functions to manipulate these structures should also be defined within this module to form an object like entity Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 22 Developer Guidelines for OpenMCTDHB Procedures should be logically flat should focus on a particular functionality not several ones Module PUBLIC variables global variables should be used with care and mostly for static or infrequently varying data Recommendations Use parentheses at all times to control evaluation order in expressions Use of structures is encouraged for a more stable interface and a more compact design Refer to structure contents with the 5 7 Vectors and Arrays Standards Subscript expressions should be of type integer only When arrays are passed as arguments code should not assume any partic ular passing mechanism Guidelines Use of arrays is encouraged as well as intrinsinc functions to manipulate them Use of assumed shapes is fine in passing vectors arrays to functions arrays Recommendations Declare DIMENSION for all non scalars 5 8 Dynamic Memory Allocation Pointers Standards Generally there is no need for pointers in the
26. ree of first order coherence 1d g2x sh Takes the last file ending on x correlations dat and plots the diagonal of Glauber s normalized second order correlation function 80 x x x x Gives a measure for the degree of second order coherence in x space 1d g2k sh Takes the last file ending on k correlations dat and plots the diagonal of Glauber s normalized second order correlation function 80 k k k k Gives a measure for the degree of second order coherence in k space 1d G2x sh Takes the last file ending on x correlations dat and plots the diagonal of Glauber s second order correlation function GO x x x x This is the density density cor relation function 1d G2k sh Takes the last file ending on k correlations dat and plots the diagonal of Glauber s second order correlation function Kk K K Kk This is the momentum momentum correlation function 1d plotprobabilityleft sh Plots the probability density in the left half of space i e the integral over the one body density from ee up to zero Scripts for 2d computations 2d density sh Collects all files ending on x density dat and plots them one after the other Allows to visualize the density in 2 dimensions Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen Chapter 5 Developer Guidelines for OpenMCTDHB These OpenMCTDHB developer guidelines are largely based on the Standards Guide lines and Recommendations for wri
27. rom default orbitals If you decide to do so it may be necessary to start with a low error tolerance e g TOLERROR 1 0E 2 and propagate the system in imaginary time until the energy of the system does not decrease any longer in the first few digits monitor the dat file contain ing the energy Then set RESTART T and increase the error tolerance in the runpars inp file Also don t forget to make the files restart orbs out and restart coef out the new input files for the orbitals and the coefficients i e replace the suffix out by inp It turns out that the ground state at the given interaction strength is to a very good approximation of the Gross Pitaevskii type To minimize the size of the directory only some of the output files were saved As expected the energy of the two orbital computation is below the Gross Pitaevskii result This can be seen by comparing the two files energyN100M1HarmonicTrap 2d GS dat and energyN100M2HarmonicTrap 2d GS dat You can also plot the densities of the two solutions using the script 2d density sh Please see the scripts section of this manual This completes our second worked through example The current manual has hopefully helped the new user to get started with with OpenMCTDHB It is also a good idea to read through the code documentation on the OpenMCTDHB website Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen Chapter 4 Scripts This Chapter documents the
28. s as follows We will illustrate it using the example BJJ propagation 1d of the examples directory In this particular example a purely coherent condensate of one hundred particles resides initially in the left well of a double well potential and sub sequently tunnels through the barrier The interaction strength is weak e create a directory TEST BJJ propagation 1d Let s say for simplicity in the OpenMCTDHBv2 1 directory where also the executables are cd into the TEST BJJ propagation 1d directory and copy all the inp files from examples BJJ propagation 1d input there i e the files restart orbs inp restart coef inp runpars inp and V extinp e create a symbolic link to or copy OpenMCTDHB x in the directory type OpenMCTDHB x the program should now start running While you are eagerly waiting for results or after the program has finished you can analyze the output You will need gnuplot for the following scripts to work open another shell and cd into the TEST BJJ propagation 1d directory Assuming the program is still running there should be a growing number of files there 8 Basic Usage e create a symbolic link to the scripts directory type In s scripts type scripts 1d x density sh 60 to plot the one body density at different time points The value 60 determines the largest value on the y axis of the plot the time difference between plots depends on the variable pr
29. scripts in the scripts directory As a general advice it is a good idea to create a symbolic link In s path to the scripts directory to the scripts directory in any directory in which a computation was carried out gnuplot is used as the plotting program Make sure you have a reasonably new version of it Square brackets indicate optional arguments 4 1 4 2 Scripts for any number of dimensions plotnoccs sh plots the natural orbital occupation numbers as a function of time Scripts for 1d computations 1d x density sh maximal y value Collects all files ending on x density dat and plots them one after the other The one body densities of the system 1d k density sh maximal y value Collects all files ending on k density dat and plots them one after the other The one body momentum distributions of the system 1d x densitydynamics sh Collects all files ending on x density dat concatenates them and plots them in a 2D plot Allows to visualize the time evolution the one body density of the system 1d k densitydynamics sh Collects all files ending on k density dat concatenates them and plots them in a 2D plot Allows to visualize the time evolution of one body momentum distribution of the system 1d gix sh Takes the last file ending on x correlations dat and plots the absolute value squared 16 Scripts 4 3 of Glauber s normalized first order correlation function g x x Allows to vi sualize the deg
30. ting Fortran 95 codes of S A Boukabara and P van Delst and are tailored specifically to OpenMCTDHB Prospective developers if you would like to contribute to OpenMCTDHB please contact the developers Current developers it is likely that very soon there will be an official roadmap of Open MCTDHB However right now the roadmap is only very loosely defined Therefore please coordinate with the other developers before writing any new code 5 1 Introduction The purpose of this document is to ensure that new Fortran95 additions to OpenMCT DHB will be as portable and robust as possible as well as consistent throughout the System It builds upon experience to avoid error prone practices and gathers guidelines that are known to make codes more robust This document covers items in order of decreasing importance see below Standards Aimed at ensuring portability readability and robustness Compliance with this category is mandatory Identified by the sign Guidelines Good practices Compliance with this category is strongly encour aged The case for deviations will need to be argued by the programmer Identi fied by the sign Recommendations Compliance with this category is optional but is encouraged for consistency purposes No sign for these items 18 Developer Guidelines for OpenMCTDHB Please adhere to the standards religiously This document also lists a set of Fortran features that are not to be used i
31. to the ground state given you have some input files for the orbitals and the coefficients Here is a list ing of such a file for a two orbital computation taken from the examples HarmonicTrap 2d directory amp SYSTEMPARAMETERS LAMBDAO 0 01 NPAR 100 MORB 2 DIMS 2 USEIMEST F amp IMESTPARAMETERS IMESTPARAMETER1 5 00000000000000028bE 002 amp GRIDPARAMETERS 6 000000000000000 6 000000000000000 6 0000000000000000 YF 6 0000000000000000 Zl 0 0000000000000000 ZF 0 0000000000000000 NDX 64 NDY 64 NDZ das zh amp PRINTPARAMETERS TINYSTEP 0 10000000000000001 PRINTSTEP 5 0000000000000000 Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 14 Basic Usage PRINTALLSTEP 100 0000 PRINTCORRELATIONFUNCS 0 amp RUNPARAMETERS ABSTIME 0 000000000000000 MAXTIME 100 000000000000000 TOLERROR 1 00000000000000022E 008 RESTART T RELAX T READPOTENTIAL T PROPDIRECTION 1 TAG HarmonicTrap 2d GS It is recommended to use the files restart orbs_MORB2 out restart coef_MORB2 out as input files for the two orbital computation and the files restart orbs_MORB1 out restart coef_MORB1 out for the one orbital computation These files already contain the solution to the respective problems However you do not necessarily have to provide any orbitals or coefficients if you set RESTART F in runpars inp The program will then start f
32. ts format is the same for 1D 2D and 3D problems The first three columns contain the values of x y and z while the fourth column contains the corresponding value V x y z x is the fast running variable i e y is increased only once x has run from the first to last grid point in the x direction Similarly z is increased once y has run once from its first to the last grid point You can create the v extinp file using the program V ext x see below 3 2 3 The file restart orbs inp The file restart orbs inp contains the orbitals of the wave function Its format is the same for 1D 2D and 3D problems The first three columns contain the values of x y and z while the fourth column contains the corresponding value V x y z The next two columns contain the real and imaginary parts of the first orbital and if MORB 2 the next two columns the respective values of the second orbital Generated on Sun Mar 13 2011 15 19 57 for OpenMCTDHB by Doxygen 12 Basic Usage 3 24 The file restart coef inp The file restart coef inp contains three columns The first column contains the index of a configuration whereas the second and third column contain the real and imaginary part of the corresponding coefficient 3 3 How to setup a new problem It is now assumed that you have a working version of OpenMCTDHB installed that reproduces the results of the examples directory We will now discuss a convenient way to set up a new problem assuming

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