Home

USER MANUAL

Contents

1. bondforcepolynomial setParams polymer 10 0 100 0 1 2 sets parameters by bond type spring constant spring constant equilibrium bond length app add bondforcepolynomial adds this object to the application 6 3 4 Angle harmonic force Constructor AngleForceHarmonic boost shared ptr AllInfo note specifies the angle harmonic force parameter AllInfo Functions void setParams const std string amp Real Real note specifies the angle harmonic force parameters parameters angle type spring constant equilibrium angle degree Example angleforce galamost AngleForceHarmonic all info initializes AngleForceHarmonic object by AllInfo object angleforce setParams P G G 25 000 120 000 sets parameters by angle type spring constant equilibrium degree app add angleforce adds this object to the application 6 3 5 Angle cosine harmonic force Constructor AngleForceHarmonicCos boost shared ptr AllInfo Command Index 25 note specifies the angle cosine harmonic force parameter AllInfo Functions void setParams const std string amp Real Real note specifies the angle cosine harmonic force parameters parameters angle type spring constant equilibrium angle degree Example angleforce galamost AngleForceHarmonicCos all_info initializes AngleForceHarmonic object by AllInfo object angleforce setParams P G G 25 000 120 000 sets parameters by angle type spring constant equilibrium
2. double double note specifies the period upper and lower bounds at the time step parameters time step period upper and lower bounds Example v galamost VariantSin initializes VariantSin object v setPoint 0 1000 1 0 1 0 v setPoint 100000 1000 2 0 2 0 set the parameters of sinusoid at the time step and the parameters at any time step can be gotten by linear interpolation 6 8 6 Variant Well Constructor VariantWell note specifies well curve varing method Functions void setPoint unsigned int double double double note specifies the period upper and lower bounds at the time step parameters time step period upper and lower bounds Example v galamost VariantWell initializes VariantWell object Command Index 42 v setPoint 0 1000 1 0 1 0 v setPoint 100000 1000 1 0 1 0 set the parameters of periodic well at the time step and the parameters at any time step can be gotten by linear interpolation 6 9 Some functional modules 6 9 1 The coarse graining numerical method 1 Non bonded interaction Constructor PairForceTable boost shared_ptr lt AllInfo gt boost shared_ptr lt NeighborList gt unsigned int note specifies the method of numerical pair force parameters AllInfo NeighborList the number of potential points Functions void setParams const std string amp const std string amp Real const std string amp int int note specifies the numeri
3. sets parameters by bond type spring constant equilibrium bond length app add bondforce adds this object to the application 6 3 2 Bond fene force Constructor BondForceFene boost shared ptr AllInfo note specifies the FENE bond force parameter AllInfo Functions void setParams const std string amp Real Real note specifies the FENE bond force parameters parameters bond type spring constant maximum length of the bond void setParams const std string amp Real Real Real Real note specifies the FENE LJ bond parameters parameters bond type spring constant maximum length of the bond epsilon sigma Example bondforcefene galamost BondForceFene all_info initializes BondForceFene object by AllInfo object bondforcefene setParams polymer 10 1 2 sets parameters by bond type spring constant maximum length of the bond app add bondforcefene adds this object to the application 6 3 3 Bond polynomial force Constructor BondForcePolynomial boost shared_ptr lt AllInfo gt note specifies the polynomial bond force parameter AllInfo Functions void setParams const std string amp Real Real Real Command Index 24 mote specifies the polynomial bond force parameters parameters bond type spring constant k spring constant kz equilibrium bond length Example bondforcepolynomial galamost BondForcePolynomial all info initializes BondForceFene object by AllInfo object
4. std string double note specifies the bond length of the bond which connect two kind particles Command Index 51 parameters particle type 1 particle type2 bond length void setAngleDegree std string std string std string double note specifies the angle degree of the angle consisting of three kind particles parameters particle type 1 particle type2 particle type3 angle degree void setAngleDegree unsigned int unsigned int unsigned int double note specifies the angle degree of the angle consisting of three particles parameters particle 1 particle 2 particle 3 angle degree void setDihedralDegree std string std string std string std string double note specifies the dihedral degree of the dihedral consisting of four kind particles parameters particle type 1 particle type2 particle type3 particle type4 dihedral degree void setDihedralDegree unsigned int unsigned int unsigned int unsigned int double note specifies the dihedral degree of the dihedral consisting of four particles parameters particle 1 particle 2 particle 3 particle 4 dihedral degree void setMass double note specifies the mass of all kind particles parameters mass void setMass std string double note specifies the mass of the kind particle parameters particle type mass void setMass unsigned int double note specifies the mass of the particle parameters particle index mass void setChar
5. 6 2 3 v o a 1 2 r Q harmonic ij 2 r cut 3 2 where a and rcut set the maximum energy penalty and maximum interaction distance respectively Gaussian repulsion CI 6 2 3 2 ix U caussion Ny exp AM Z 2 o 3 3 Force Fields 8 where and o determine the energy and length scales respectively 3 2 Bonded forces The bonded forces generally include the bond angle and torsion forces Because of the execution mode of SIMD in GPU it is efficient that a thread calculates and sums the bond angle and torsion forces of a particle in the kernel functions Therefore we can employ the thread whose number is equal to the number of particle to calculate the bonded forces of each particle independently Although the force of a bond will be computed twice three times for an angle and four times for a torsion on device it casts the computation well into parallel mode for separated threads of GPUs and is efficient for data copy between host and device memories The common bonded potential energy functions in GALAMOST are Bond harmonic CI 6 3 1 I bond 2 U oa rj 2 r v n 3 4 Bond FENE CI 6 3 2 2 bond 2 rj Usona 0 Zk 47 log 1 2 r s 3 5 Bond polynomial CI 6 3 3 __ 7 bond 2 bond 4 Uu Uj Ky TY tk n 3 6 in which r is the instantaneous length of the bond ro is the equilibrium length bond of the bond rnis maximum length and is the spring cons
6. Functions void setT Real note specifies the temperature Command Index 29 parameters a fixed value of temperature void setT boost shared ptr Variant note specifies the temperature parameters a defined varing temperature according to time steps Example an galamost AndersenNvt all info group 1 0 10 0 12345 initializes AndersenNvt object by AllInfo object ParticleSet object temperature collision frequency RNG seed app add an adds this object to the application 6 4 5 Npt ensemble with Andersen barostat Constructor Npt boost shared ptr AllInfo boost shared_ptr lt ParticleSet gt boost shared_ptr lt ComputeInfo gt boost shared_ptr lt ComputelInfo gt Real Real Real Real note specifies the NPT thermostat of a group of particles parameter AllInfo ParticleSet ComputeInfo ComputeInfo temperature pressure tauT tauP Functions void setP Real note specifies the pressure parameters a fixed value of pressure void setT Real note specifies the temperature parameters a fixed value of temperature void setT boost shared_ptr lt Variant gt note specifies the temperature parameters a defined varing temperature according to time steps Example npt galamost Npt all_info group comp_info comp_info 1 0 0 2 0 5 0 1 initializes Npt object by AllInfo object ParticleSet object ComputeInfo Command Index 30 object for the group ComputelInfo object for all pa
7. Linux operation system and display on terminal computer with Windows through Exceed or some other X server programs UGI is usually used to generate GALAMOST script Before doing that we should choose a XML file which contains the necessary information of the system i e particle types and bond types to help building script We can select the functions of GALAMOST and set parameters by clicks and inputs By building a project a window will be open to indicate the chosen items With it you can cancel or reset parameters At last you can generate and output a GALAMOST script Force Fields 7 3 Force Fields 3 1 Short range non bonded forces In polymer systems the net non bonded force of each particle is produced by summing all the non bonded forces of neighboring particles The standard algorithm is to use a neighbor list that lists the interacting particles for each particle built beforehand Because of the independence of parallel CUDA threads a pair of interacting particles is inevitably included independently in neighbor list in the mode that one thread calculates and sums all non bonded forces of a particle The common non bonded potential energy functions are included in GALAMOST which are Lennard Jones LJ CI 6 2 1 TORG where e is the depth of the potential well is the finite distance at which the 3 1 interparticle potential is zero and r is the distance between the particles Harmonic repulsion CI
8. able to try running GALAMOST as Jdpd gala gpu 0 a log amp where you may specify the GPU id with the gpu option and output the screen information into a log file If the script file has no executive permission the command of chmod x dpd gala should be executed before running above command Here is an example of script The head of GALAMOST script such as dpd gala usually is usr bin python import Sys sys path append opt galamost lib import galamost global options parser OptionParser parser add_option gpu dest gpu help GPU on which to execute options args parser parse_args where the first paragraph sets the path of the installed library of GALAMOST galamost so for loading the Python extensible modules of GALAMOST The second paragraph is used for parsing GPU id from the executive command Then by reading the configuration from a prepared XML file a system with necessary information can be built up by filename A xml build method galamost XmlReader filename perform config galamost PerformConfig int _options gpu all info 2 galamost AllInfo build method perform config After that we need to build up an application which will call following defined and added objects by Installation and Usage dt 0 01 app galamost Application all info dt Further we should define the needed objects by the classes of GALAMOST and pass them to the application such a
9. amp Real Real Real Real Real note specifies the LZW force parameters by pair types parameters type 1 type 2 alphaR mu nu alphaA beta void setMethod const std string amp note choses a method of Disk Janus ABAtriJanus BABtriJanus Example lzw galamost LzwForce all info neighbor list 1 0 initializes LzwForce object by AllInfo object NeighborList object cut off Izw setParams A A 396 0 1 0 0 5 88 0 60 0 180 0 3 1415926 sets parameters by typel type 2 alphaR mu nu alphaA beta Izw setMethod ABAtriJanus sets method with the choise of ABAtriJanus Command Index 48 app add lzw adds this object to the application 2 Thermostat Constructor BerendsenAniNvt boost shared_ptr lt AllInfo gt boost shared_ptr lt ParticleSet gt boost shared_ptr lt ComputeInfo gt Real Real Real note specifies the Berendsen NVT thermostat for anisotropic particles parameters AllInfo ParticleSet ComputeInfo temperature tauT tauR Functions void setTau Real Real note specifies the Berendsen NVT thermostat parameters tauT tauR void setT Real note specifies the temperature parameters a fixed value of temperature void setT boost shared_ptr lt Variant gt note specifies the temperature parameters a defined varing temperature according to time steps Example bere galamost BerendsenAniNvt all_info group comp_info 1 0 0 3 0 1 initializes BerendsenAniNvt obj
10. be added between them and then the active end should be transferred to the new end 4 3 Gay Berne particle model This model is usually used to describe ellipsoidal particles Except for translocation the rotation of these anisotropic particles has to be considered Then forces and torques are typically incorporated into molecular dynamics simulation The forces and torques are derived from Gay Berne anisotropic potential which is given here r c o l r 0o 0 3 18 3 19 Characteristic Models 14 3 20 3 21 3 22 3 23 3 24 3 25 where o is end to end length o is side to side length e is end to end energy and e is side to side energy Configuration Input 15 5 Configuration Input 5 1 Coordinate file We take XML format file as the standard inputting configuration file The xml file can contain types masses coordinates velocities topological information and so on Here is an example of XML file of 4 particles system The position data in a line x y and z directions locates a particle in box and one line corresponds to one particle in sequence This is also same rule for some other data but do not include topological information lt xml version 0 2 encoding UTF 8 lt galamost_xml gt lt configuration time_step 0 gt box unitsz sigma Lxz I0 Ly 10 Lz 10 gt position units sigma gt 12 1 230 141 52 lt position gt lt velocity un
11. degree app add angleforce adds this object to the application 6 3 6 Angle cosine force Constructor AngleForceCos boost shared_ptr lt AllInfo gt note specifies the angle cosine force parameter AllInfo Functions void setParams const std string amp Real Real note specifies the angle cosine force parameters parameters angle type spring constant equilibrium angle degree Example angleforce galamost AngleForceCos all_info initializes AngleForceCos object by AllInfo object angleforce setParams P G G 25 000 120 000 sets parameters by angle type spring constant equilibrium degree app add angleforce adds this object to the application Command Index 26 6 3 7 Dihedral harmonic force Constructor DihedralForceHarmonic boost shared_ptr lt AllInfo gt note specifies the dihedral harmonic force parameter AllInfo Functions void setParams const std string amp Real Real note specifies the dihedral harmonic force parameters parameters dihedral type spring constant equilibrium dihedral degree Example dihedralforce galamost DihedralForceHarmonic all_info initializes DihedralForceHarmonic object by AllInfo object dihedralforce setParams A B B A 10 0 0 0 sets parameters by dihedral type spring constant equilibrium degree app add dihedralforce adds this object to the application 6 3 8 Dihedral Opls Cosine force Constructor DihedralForceOplsCosine boost shared ptr A
12. erede depen o t dpa tb ede dee ta qd et 47 6 9 5 GaysBerrnednodel i di a A DU abe UE 48 6 10 Configuration generator te 50 0 11 D ta tackle c 55 7Appended DOCUTBEBES ena va tition oda dal Ba ed BA ARR 58 72 Polymerization Models sissies 58 Introduction 1 Introduction 1 1 A sketch of GALAMOST GALAMOST is a versatile molecular simulation package which is designed to utilize computational power of graphics processing units GPUs as much as possible In addition to common features of molecular dynamics programs it is developed specially for coarse graining simulation of polymeric systems by encompassing some latest techniques such as hybrid particle field molecular dynamics iterative Boltzmann inversion numerical potential method soft anisotropic particle model and chain growth polymerization model By continuously optimizing the algorithms each method implemented on a single GPU by GALAMOST has gained a good performance Some biomolecules and polymers can be modeled in coarse grained MD CGMD simulations implemented by GALAMOST The CGMD has become a powerful tool accounting for the problems related to self assembly phase separation and other phenomena of polymeric systems The choices for general force field functions in GALAMOST will be listed in the following sections In addition a hybrid particle field MD technique MD SCF for calculating intermolecular interactions has been incorporated in GALAMOST With this technique t
13. function of output of Mol2 files parameters MoD filename Example genzmolgen Generators 10 10 10 initializes Generators object by box length in x y and z direction gen addMolecule mol0 10 adds Molecule by Molecule name the number of molecules gen setParam A A 1 0 0 7 1 0 sets parameters of LJ potential which is used for Rosenblueth method gen setMinimumDistance 0 7 sets minimum seperated distance of all particles gen setMinimumDistance A A 0 7 sets minimum seperated distance between the particle types gen outPutXml test sets file name of output XML file 6 11 Data tackle The galaTackle is a tool to get some important information by analyzing the output raw data from configuration files You may call this tool by running command Command Index galaTackle particle xml where galaTackle can be found in the installed bin file and the XML configuration files should be put in current directory listed You can chose one or several functions by the number index seperated by blank and press enter to execute After the executation of above command a menu of many options will be ID Functions Paramters Description 1 Rg mean square of gyration radius 2 Ed mean square of end end distance 3 RDF maxbin 100lgpu i radial distribution function d 0 4 bond distri npot 2001 bond length distribution 3 angle distri npot 2001 angle degree distribution
14. of outputing quaternion void setOutputRotation bool note switches the function of outputing rotation velocity void setOutputTorque bool note switches the function of outputing torque void setOutputInert bool note switches the function of outputing inert tensor void setOutputInit bool note switches the function of outputing initiator indication void setOutputCris bool note switches the function of outputing cris void setOutputBond bool note switches the function of outputing bond void setOutputAngle bool note switches the function of outputing angle void setOutputDihedral bool note switches the function of outputing dihedral Example xml galamost XmlDump all info particles initializes XmlDump by AllInfo object filename xml setPeriod 100000 sets dump period Command Index 38 app add xml adds this object to the application 6 7 4 Configuration dump with dcd format Constructor DcdDump boost shared_ptr lt AllInfo gt const std string amp bool note specifies the dump method of DCD file parameters AllInfo file name overwrite former data Functions void removePbc bool note switches the function of unwrapping the molecules folded by PBC Example dcd galamost DcdDump all_info particles True initializes XmlDump object by AllInfo object filename overwriting dcd removePbc True unwraps the molecules folded by PBC dcd DedDump 100000 sets dump per
15. parameters bond type bond spring constant end to end length of GB particle angle spring constant equilibrium angle degree Example bondani galamost BondForceAni all_info initializes BondForceAni object by AllInfo object bondani setParams A A 100 0 4 498 30 0 0 0 sets parameters by bond type bond spring constant sigmae angle spring constant equilibrium angle degree Command Index 50 app add bondani adds this object to the application 6 10 Configuration generator 1 The head of script usr bin python import sys sys path append opt galamost3 lib import molgen sets the path of molgen so and imports extended Python module of molgen 2 Molecules defination Constructor Molecule unsigned int note defines a molecule by Molecule parameters the number of particles in a molecule Molecule const std string amp unsigned int note defines a molecule by Molecule and reads partial data from a file parameters file name number of particles in a molecule Functions void setParticleTypes std string note specifies the particle types seperated by comma with particle index form 0 to N 1 in sequence void setTopology std string note specifies bonds seperated by comma which connect two particles seperated by crossband void setIsotactic bool note switches the isotactic configuration of molecule void setBondLength double note specifies the bond length of all bonds void setBondLength std string
16. 0 dihedral distri npot 2001 dihedral degree distribution 7 stress tensor bondex truelbody stress tensor ex falselrcut 3 0 8 density density in real unit 9 re cal image removes PBC and keeps the center mass in box 10 MSD mean square displacement of all particles 11 RDFcu maxbin 100lgpu i the RDF of center mass of d 0 molecules 12 MSDcm the MSD of center mass of molecules Command Index 57 13 ents analyzing entanglement information of long chains 14 strfac kmax 80 gpu_id structure factor 0 15 domain size kmax 20lqc 0 46 domain size 90lgpu id 0 16 dynamic strfac kmax 20lq 7 0 dynamic structure factor 17 config check bondex truelbody checks the configuration ex falselrcut 2 0 from XML file Appended Documents 58 7 Appended Documents 7 1 Polymerization model 1 2 Wisk AAAA AS gt AAAAA reaction galamost Polymerization reaction setPr A A 0 005 reaction setPeriod 50 app add reaction ik reaction setMaxCris A 2 reaction setPr A B 0 005 A C
17. C A C h_init 1 A h_cris 0 C h_cris gt 1 h_cris J amp 1 1 h init GPU h_cris h_cris 0 h_cris 1 h_cris setMaxCris h_init 1 A B C A B C A B C A C B reaction setExchangePr A B C0 1 reaction setExchangePr AcC B 0 1 B Cc Y 2
18. GALAMOST GPU Accelerated Large Scale Molecular Simulation Toolkit CLEANLGA USER MANUAL Version 0 0 3 Contents Contents J Tntroduetion s ausa d abide nd ae dU o ndi prepa d rp dU E 1 IIA Sketc hgr GAL ANIONS T sm tates neat bet etel ta moo abba toc el tiun 1 2 Installation and Usage ee 3 2 1 Compiling and mstallation us eontra iet etd ee sa a a aaa 3 22 Usage by Spt aic adeicouegtiat i pce essen aoaaa eit ita Tace can abba oec ee ii TNe 3 2 3 Usage by user graphic interface nn 6 3 Force FleldS mb ne E R 7 3 1 Short range non bonded forces iia e ciet bec bl a Re dice a citta idu a dad n 7 2 2 BOnded PONCE S vod s ai Oa dusts E Ce RU dtd n OR quse s E dba sea anatase eee n 8 Dao Numerical TOO Sa en de mn a a e a a a aa a aT aa aaae a 10 4 Characteristic Models ases titus otto etia aiat edt i 12 4 1 Soft anisotropic particle model nn 12 4 2 Polymerization TOdel iudici odit aiaa 13 4 3 Gay Berne particle model ee 13 3 Configuration Input iiir ret rr nh a re e ERR ede 15 S Coordinate TTG un lnean e de 15 5 2 TODOLOPIES iaaea e tse oni aeara 16 6 Command Index 25 ovp OE erent 18 6 1 Reading the initial configuration of system sse 18 6 INE Sir geris T 18 021 2 BIN paset a eee roin pectus enia A te ege d OPERE RAR shale prn Du eE abba aug endi 18 6 2 NOME Donde TOMES ea ed Ub qai eA tice Du loda d qur 18 NEN T M 18 62 2 DPD Orce oif bins kd pee itd di a equ e eda eed
19. Mol2Dump all info particles initializes Mol2Dump object by AllInfo object base file name mol2 setPeriod 100000 sets dump period mol2 deleteBoundaryBond True undisplays the bonds which across the box app add mol2 adds this object to the application 6 7 3 Configuration dump with xml format Constructor XmlDump boost shared ptr AllInfo std string note specifies the dump method of XML files parameters AllInfo base file name Functions void setOutputPosition bool note switches the function of outputing position the default is true void setOutputType bool note switches the function of outputing type the default is true void setOutputImage bool note switches the function of outputing image void setOutputVelocity bool note switches the function of outputing velocity void setOutputMass bool note switches the function of outputing mass void setOutputCharge bool note switches the function of outputing charge void setOutputDiameter bool note switches the function of outputing diameter Command Index 37 void setOutputBody bool note switches the function of outputing body void setOutputVirial bool note switches the function of outputing virial void setOutputForce bool note switches the function of outputing force void setOutputOrientation bool note switches the function of outputing orientation void setOutputQuaternion bool mote switches the function
20. NG seed Functions void setGamma Real note specifies the gamma of Brownian method parameters a fixed value of gamma void setGamma const std string amp Real note specifies the gamma of Brownian method of different types parameters type gamma void setT Real note specifies the temperature parameters a fixed value of temperature void setT boost shared_ptr lt Variant gt note specifies the temperature parameters a defined varing temperature according to time steps Example bdrigidnvt galamost BdNvtRigid all_info bgroup 1 0 123 initializes BdNvtRigid object by AllInfo object ParticleSet object temperature RNG seed app add bdrigidnvt adds this object to the application 6 4 9 Nve rigid body thermostat with tunable freedoms Constructor TranRigid boost shared_ptr lt AllInfo gt boost shared_ptr lt ParticleSet gt Command Index 32 note specifies the NVE thermostat of rigid bodies in defined freedoms parameter AllInfo ParticleSet Functions void setTraDimention bool bool bool note switches the freedoms of translocation in x y z directions parameters True or False for x y z translocation respectively void setRotDimention bool bool bool note switches the freedoms of rotation in x y z directions parameters True or False for x y z rotation respectively Example bdrigidnvt galamost TranRigid all info bgroup initializes TranRigid object by AllInfo object Part
21. UNDA 32 65 T Bark eroup Dy Keyword S4 ioo tege desi ede e e ena ete x tete 32 6 5 2 Build group by index range Of particles eee 33 O09 3 COmbine PEDUDS a 33 6 0 Particle LSE ai a dd a de a Ee La EM exu s 33 6 0 T Build neghbordists ssn a bdo e Ep re M edi anti niet 33 6 0 4 Dutld cell Ista acte a a tet i SOR oda erae ta tte e eu qe be QR 34 6 7 iret ENS 35 6 7 1 The dump of some important informations Ne 35 6 7 2 Configuration dump with mol2 format esee 35 6 7 3 Configuration dump with xml format eee 36 6 7 4 Configuration dump with dcd format eee 38 6 7 5 Configuration dump with binary format eee 38 6 0 SOME Other FUDCUQS didi rr tied tite det esas deed ed ci eiie ptu ai 39 6 8 1 Removing the momentum of center of mass ee 39 Contents 6 8 2 The computition of some important informations eee 39 6 9 3 SOLUDE data neue ici ei eoa Loeb da aa A Fd eae bret ia e d 40 6 824 Variant gmeat iie a ERO eH NR aiea ani E 40 6 5 3 VALAIS Le eaae eicit etie Delo iden e breui Be vetat de uie Er T ee 41 65 5 Variant Wells cot use rti ameta ttis dert d setas a ies dtd 41 6 9 Some functional modules edet ee enini Inde g eco ee bem adlata PE Ce UH e dogs 42 6 9 1 The coarse graining numerical method se 42 6 9 2 The MD SCF method re a eataa i aa ainan taaa iTA 44 6 9 3 The Polymerization method iso oodd bo pote Popoli ecco eis 45 6 94 AisotrOpic Tode sy pite ed
22. ao dus bread aperte 19 6 2 3 Pair force for LJ12 6 LJ9 6 harmonic Gauss eee 20 6 24 External POLE NE a ea OT 21 6 3 Bonded TOTES sn de ee aar aea ani 22 6 3 T Borid harmonie TORCE ds deep tage atate qeefen a 22 6 3 2 Bond fene fOrCO cecccccccesscccccesscccccesscccecesscceccesscceecesscceeeesseceesesseceeeesseceeeees 23 Contents 6 3 2 Bond polynomial force eir pns aided nates ede gi eda io eie besser 23 6 3 4 Angle harmonie TOrCe si en eoi o PR a ERR NAR USER E ERRARE E DIRE dM Me dA 24 6 3 5 Angle cosine harmonic force pp 24 GSO mele COSTI FOPCER oder ele ren eei iic De a a teach 25 6 37 Dihedralharmotio POLICE den d dn dents a iesu 26 6 3 8 Dihedral Opls Cosine forCe eed dot ice tie qti ag eet te itae etai eque 26 6 4 Integration methods css i do oa Na ANN SNR Vra ud eed Ro nus aa eua 27 6 4 1 Nye ensemble ace oos dept ee 27 6 4 2 Nvt ensemble with Nose Hoover method 0 27 6 4 3 Nvt ensemble with Berendsen method pp 28 6 4 4 Nvt ensemble with Andersen method nn 28 6 4 5 Npt ensemble with Andersen barostat esee 29 6 4 6 Nve rigid body thermostat ses deni e epe eder eid den ea se brava derat da 30 6 4 7 Nvt rigid body thermostat oisi risen eed agree i prr dag Rin en 30 6 4 8 Brownian dynamic nvt rigid body thermostat ppp 31 6 4 9 Nve rigid body thermostat with tunable freedoms 31 6 5 Partic Ie CIPOUD oe tte studens etapa us DER E TE Falc taa etude NOR
23. cal pair interaction parameters by pair types parameters type 1 type 2 cut off inputting file name start column end column Example pair galamost PairForceTable all_info neighbor_list 1 3 2000 initializes PairForceTable object by AllInfo object NeighborList object cut off the number of inputting data pair setParams A A 1 3 table dat 0 3 sets parameters by type 1 type 2 cut off inputting file name start column end column four columns for C C C3 C4 app add pair adds this object to the application 2 Bond interaction Constructor BondForceTable boost shared ptr AllInfo Real unsigned int Command Index 43 note specifies the method of numerical bond force parameters AllInfo cut off the number of potential points Functions void setParams const std string amp const std string amp int int note specifies the numerical bond interaction parameters by bond types parameters bond type inputting file name start column end column Example bond galamost BondForceTable all info 2 0 2000 initializes BondForceTable object by AllInfo object cut off data number bond setParams 1 1 table dat 0 3 sets parameters by bond type cut off inputting file start column end column app add bond adds this object to the application 3 Angle interaction Constructor AngleForceTable boost shared ptr AllInfo unsigned int note specifies the method of numerical angle for
24. ce parameters AllInfo the number of potential points Functions void setParams const std string amp const std string amp int int note specifies the numerical angle force parameters by bond types parameters angle type inputting file name start column end column Example angle galamost AngleForceTable all_info 500 initializes AngleForceTable object by AllInfo object data number angle setParams 111 table dat 0 3 sets parameters by angle type inputting file start column end column app add angle adds this object to the application 4 Dihedral interaction Command Index 44 Constructor DihedralForceTable boost shared ptr AllInfo unsigned int note specifies the method of numerical dihedral force parameters AllInfo the number of potential points Functions void setParams const std string amp const std string amp int int note specifies the numerical dihedral force parameters by dihedral types parameters dihedral type inputting file name start column end column Example dihedral galamost DihedralForceTable all_info 500 initializes DihedralForceTable object by AllInfo object data number dihedral setParams 111 table dat 0 3 sets parameters by dihedral type inputting file start column end column app add dihedral adds this object to the application 6 9 2 The MD SCF method Constructor MdScfForce boost shared_ptr lt AllInfo gt unsigned int unsigned
25. cle index void setRadius double note specifies the radius of the sphere which will be generated parameters radius Example mol0 molgen Object sphere2 xml 65 molgen Object Shape sphere initializes Object object by the reading file the number of particles shape mol0 setParticleTypes C 60 A 5 sets particle types molO setTopology 59 60 60 61 61 62 62 63 63 64 sets topology molO setBody C sets body particles 4 Generator defination Constructor Generators double double double note specifies a generator by Generators parameters box length in x y z directions Functions void addMolecule boost shared_ptr lt Molecule gt unsigned int note adds molecules into generator parameters Molecule the number of molecules void setMinimumDistance double note sets minimum seperated distance of all particles Command Index 55 void setMinimumDistance const std string amp const std string amp double note sets minimum seperated distance of two kind particles parameters particle type 1 particle type 2 minimum distance void setParam const string amp const string amp double double double note sets LJ potential parameters between two kind particles for Rosenblueth method parameters particle type 1 particle type 2 epsilon sigma cut off void outPutXml std string note switch on the function of output of XML files parameters XML filename void outPutMol2 std string note switch on the
26. d_ptr lt ParticleSet gt combine boost shared_ptr lt ParticleSet gt boost shared_ptr lt ParticleSet gt note combines two groups into one parameter ParticleSet ParticleSet Example groupAB galamost ParticleSet combine groupA groupB initializes ParticleSet object by ParticleSet object ParticleSet object 6 6 Particle List 6 6 1 Build neighbor list Constructor NeighborList boost shared_ptr lt AllInfo gt Real Real note specifies the neighbor list of all particles parameters AllInfo cut off buffer distance Command Index 34 Functions void setRCut Real Real note specifies the cut off and buffer distance parameters cut off buffer distance void setNsq note switches on the method of searching all particles to build up list void setDataReproducibility note switches on the data reproducibility Example neighbor list 2 galamost NeighborList all info 3 0 0 4 initializes NeighborList object by AllInfo object cut off buffer distance 6 6 2 Build cell list Constructor CellList boost shared ptr AllInfo note specifies the cell list of all particles parameter AllInfo Functions void setNominalWidth Real note specifies the length of cell parameters the length of cell void setNominalDim unsigned int unsigned int unsigned int note specifies the dimentions of grid in x y z directions respectively parameters the number of cells in x y z directions void setDataReproduc
27. ect by AllInfo object NeighborList object ParticleSet object ComputeInfo object temperature tauT tauR app add bere adds this object to the application 6 9 5 Gay Berne model 1 GB Pair Force Constructor GBForce boost shared_ptr lt AllInfo gt boost shared_ptr lt NeighborList gt Real note specifies the method of Gay Berne force parameters AllInfo NeighborList cut off Command Index 49 Functions void setParams const std string amp const std string amp Real Real Real Real Real Real Real Real Real note specifies the GB force parameters by pair types parameters typel type 2 epsilonO sigma0 nu mu end to end length sigmae side by side length sigmas end to end energy epsilone side by side energy epsilons Ps Example gb galamost GBForce all_info neighbor list 10 0 initializes GBForce object by AllInfo object NeighborList object cut off gb setParams A A 1 5 1 5 1 0 2 0 3 0 1 0 0 5 3 0 1 0 sets parameters by type 1 type 2 epsilonO sigma0 nu mu sigmae sigmas epsilone epsilons Ps app add gb adds this object to the application 2 Bond Force of anisotropic particles Constructor BondForceAni boost shared_ptr lt AllInfo gt note specifies the method of bond force of anisotropic particles parameters AllInfo Functions void setParams const std string amp Real Real Real Real note specifies the bond force parameters by bond types
28. erO parameterl1 parameter2 cut off function type Function type Parameter 0 Parameter 1 Parameter 2 Command Index 21 1j12 6 epsilon sigma alpha 1j9_6 epsilon sigma alpha harmonic alpha gauss epsilon sigma Example pair galamost PairForce all_info neighbor_list initializes PairForce object by AllInfo object NeighborList object pair setParams A A 1 0 1 0 1 0 3 0 galamost PairForce Func 1j12_6 sets parameters by type 1 type 2 epsilon sigma alpha LJ12 6 function pair setParams A B 1 0 1 0 1 0 3 0 galamost PairForce Func 1j9 6 sets parameters by type 1 type 2 epsilon sigma alpha LJ9 6 function pair setParams B B 1 0 1 0 1 0 3 0 galamost PairForce Func 1j12_6 sets parameters by type 1 type 2 epsilon sigma alpha LJ12_6 function app add pair adds this object to the application 6 2 4 External force Constructor ExternalForce boost shared ptr AllInfo boost shared_ptr lt ParticleSet gt note specifies the external force for the group particles parameters AllInfo ParticleSet Functions void setForce boost shared_ptr lt Variant gt std string note specifies the force magnitude varing by time steps and direction parameters Variant and direction candidates are X Y and Z void setForce boost shared_ptr lt Variant gt Real Real Real note specifies the force magnitude varing by
29. es the reaction probability according to bond potential parameters enable or disenable this method spring constant equilibrium length for harmonic interaction or maximum length for FENE interaction the energy to shift bond potential type harmonic or FENE void setMinDisReactRule bool note switches the reaction rule of nearest reaction or near reaction parameters True for nearest reaction void initExPoint note switches on initializing reactive point for exchange reaction Example reaction galamost Polymerization all_info neighbor_list 1 12246 16361 initializes Polymerization object by AllInfo object NeighborList object cut off RNG seed reaction setFuncReactRule True 1250 000 1 0 0 470 10 0 galamost Polymerization Func harmonic Command Index 47 sets the bond connection method after reaction and conveys parameters by function rule kO r0 bO epsilon function type reaction setPr 0 002 sets the reaction probability reaction setMaxCris B 3 sets the connected bond uplimit number reaction setPeriod 50 sets the reaction period app add reaction adds this object to the application 6 9 4 Anisotropic model 1 Force and torque Constructor LzwForce boost shared_ptr lt AllInfo gt boost shared_ptr lt NeighborList gt Real note specifies the method of LZW force parameters AllInfo NeighborList cut off Functions void setParams const std string amp const std string
30. ge double note specifies the charge of all kind particles parameters charge void setCharge std string double note specifies the charge of the kind particle parameters particle type charge Command Index 52 void setCharge unsigned int double note specifies the charge of the particle parameters particle index charge void setOrientation double note specifies the orientation of all kind particles parameters orientation void setOrientation std string double note specifies the orientation of the kind particle parameters particle type orientation void setOrientation unsigned int double note specifies the orientation of the particle parameters particle index orientation void setDiameter double note specifies the diameter of all kind particles parameters diameter void setDiameter std string double note specifies the diameter of the kind particle parameters particle type diameter void setDiameter unsigned int double note specifies the diameter of the particle parameters particle index diameter void setCris unsigned int note specifies the cris of all kind particles parameters cris void setCris std string unsigned int note specifies the cris of the kind particle parameters particle type cris void setCris unsigned int unsigned int note specifies the cris of the particle parameters particle index cris void setInit unsigned int C
31. h_init 1 B 0 005 B A 0 reaction setPr A B 0 005 B setPr 0 005 0 005 grafting to 1 ABBBB gt I ABBB 1 A reaction galamost Polymerization all info neighbor list 1 2 16361 reaction setPr l A 0 005 reaction setMaxcCris I 1 reaction setMaxCris A 2 reaction setPeriod 200 app add reaction reaction setPr l A 0 005 RE Ch initz1 A 0 005 A 1 0 reaction setPr l A 0 005 A reaction setMaxCris 1 1 cris 1 is
32. he most computational time consuming parts in MD ie the intermolecular pair interactions are replaced by interactions of particles with density fields It will greatly speed up some slowly evolving collective processes in MD simulations such as micro phase separation and self assembly of polymeric systems In addition to analytical potentials numerical potential can be used in GALAMOST by reading the potential table derived from iterative Boltzmann inversion IBI method or other structure based coarse graining methods The IBI method derives the coarse grained potentials by mapping the structural distributions onto the ones obtained either from atomistic simulations or from experiments With this bottom up coarse graining scheme the derived coarse grained numerical Introduction potentials can be applied in larger systems but under the same thermodynamic conditions Besides some basic functions of general MD such as CGMD Brownian dynamics BD and dissipative particle dynamics DPD GALAMOST also encompasses several tailor made modules a soft anisotropic particle model has been incorporated for modeling some kinds of anisotropic particles and a stochastic chain growth polymerization reaction model has been developed specially for the studies related to polymerization By using these advanced simulation techniques on the GPU GALAMOST enriches the routes for researchers to investigate polymeric systems via computer simulations I
33. ibility note switches on the data reproducibility function Example cell list galamost CellList all info initializes CellList object by AllInfo object Command Index 35 6 7 Data dump 6 7 1 The dump of some important informations Constructor DumpInfo boost shared_ptr lt AllInfo gt boost shared_ptr lt ComputeInfo gt const std string amp note specifies the information dump method of a group of particles parameters AllInfo ComputeInfo file name Functions void dumpAnisotropy note switches on the dump of information related to anisotropic particles void dumpVirialEnergy boost shared_ptr lt Force gt note switches on the dump of energy and virial of inputting force object parameters Force object Example dInfo galamost DumplInfo all info comp info data log initializes DumpInfo object by AllInfo object ComputeInfo object file name dInfo setPeriod 200 sets dump period app add dInfo adds this object to the application 6 7 2 Configuration dump with mol2 format Constructor Mol2Dump boost shared ptr AllInfo std string note specifies the dump method of mol2 files parameters AllInfo file name Functions void setChangeFreeType const std string amp note specifies the type of free particles which will be changed to be F Command Index 36 void deleteBoundaryBond bool note switches on the function of undisplaying the bonds across the box Example mol2 galamost
34. icleSet object bdrigidnvt setTraDimention True True True switches the freedoms of translocation in x y z directions bdrigidnvt setRotDimention True True True switches the freedoms of rotation in x y z directions app add bdrigidnvt adds this object to the application 6 5 Particle Group 6 5 1 Build group by keywords Constructor ParticleSet boost shared_ptr lt AllInfo gt const std string amp note specifies the group of particles by keywords parameter AllInfo keywords Example groupC galamost ParticleSet all info C initializes ParticleSet object by AllInfo object particle type groupB galamost ParticleSet all info body initializes ParticleSet object of body particles by AllInfo object key word groupNB galamost ParticleSet all info non body Command Index 33 initializes ParticleSet object of nonbody particles by AllInfo object key word groupC galamost ParticleSet all info all initializes ParticleSet object of all particles by AllInfo key word 6 5 2 Build group by index range of particles Constructor ParticleSet boost shared_ptr lt AllInfo gt unsigned int unsigned int note specifies the group of particles in a range of indexes parameter AllInfo minimum index maximum index Example groupC galamost ParticleSet all info 0 10 initializes ParticleSet object by AllInfo object min particle index max particle index 6 5 3 Combine groups Functions boost share
35. int unsigned int Real note specifies the method of MD SCF force parameters AllInfo grid number in x y z direction compressibility Functions void setParams const std string amp const std string amp Real note specifies the MD SCF interaction parameters by pair types parameters type 1 type 2 y parameter void setNew Version bool note switches the function of newly developed method of implementation Example scf galamost MdScfForce all info 22 22 22 0 100 initializes MdScfForce object by AllInfo object grid number in x y z directions compressibility Command Index 45 scf setParams N N 0 000 sets parameters by typel type 2 y parameters scf setParams N 1 500 sets parameters by typel type 2 x parameters scf setParams P P 0 000 sets parameters by typel type 2 x parameters scf setPeriodScf 1 300 sets parameters by computing period of density field updating period of density field scf setNew Version True switches to newly developed version app add scf adds this object to the application 6 9 3 The Polymerization method Constructor Polymerization boost shared ptr AllInfo boost shared_ptr lt NeighborList gt Real unsigned int note specifies the method of polymerization parameters AllInfo NeighborList cut off RNG seed Polymerization boost shared_ptr lt AllInfo gt const std string amp Real boost shared_ptr lt NeighborL
36. iod app add dcd adds this object to the application 6 7 5 Configuration dump with binary format Constructor DcdDump boost shared_ptr lt AllInfo gt const std string amp bool note specifies the dump method of DCD file parameters AllInfo file name overwrite former data Functions void setOutputAIl mote switches on the function of outputing all data void setOutputForRestart note switches on the function of outputing data needed for restarting void enableCompression bool Command Index 39 note switches the function of compressing output file Example binary galamost BinaryDump all_info particle initializes BinaryDump object by AllInfo object filename binary setPeriod 10000 sets dump period app add binary adds this object to the application 6 8 Some other functions 6 8 1 Removing the momentum of center of mass Constructor ZeroMomentum boost shared_ptr lt AllInfo gt note specifies the method of making the momentum of center mass of all particles to be zero parameter AllInfo ZeroMomentum boost shared_ptr lt AllInfo gt boost shared_ptr lt ParticleSet gt note specifies the method of making the momentum of center mass of a group of particles to be zero Example zm galamost ZeroMomentum all_info initializes ZeroMomentum object by AllInfo object zm setPeriod 10 sets computing period app add zm adds this object to the application 6 8 2 The computition of some imp
37. ist gt Real unsigned int note specifies the method of polymerization with a percent of initiator parameters AllInfo type percent NeighborList cut off RNG seed Functions void setPr Real note specifies the reaction probability void setPr const std string amp const std string amp Real note specifies the reaction probability between two kind particles parameters particle type 1 particle type 2 probability void setPrFactor Real note specifies the reaction probability factor of factor where n is the times Command Index 46 the reactive end has reacted void setPrFactor const std string amp const std string amp Real note specifies the reaction probability factor between two kind particles parameters particle type 1 particle type 2 probability factor void setExchangePr const std string amp const std string amp const std string amp Real note specifies the reaction probability of replacing particle 3 to connect to paritlce 2 by particlel parameters particle type 1 particle type 2 particle type 3 probability void setMaxCris const std string amp unsigned int note specifies the upper limit number of bonds generated by reaction parameters particle type upper limit number void setNewBondType const std string amp note specifies the new bond type generated by reaction parameters bond type void setFuncReactRule bool Real Real Real Real Func note specifi
38. its sigma tau gt 123 100 3 21 Configuration Input QI lt velocity gt lt type gt A B B A lt type gt lt mass gt 1 0 2 1 0 1 0 lt mass gt lt configuration gt lt galamost_xml gt 5 2 Topologies lt bond gt polymer 0 1 polymer I 2 polymer 2 3 lt bond gt Topological information also can be inputted to program by XML file As Configuration Input above example each bond connection should be given in one line In addition to bond connection angle and dihedral information also should be given explicitly in XML as following format if they are needed angle theta 0 1 2 theta 1 2 3 angle lt dihedral gt phid 123 lt dihedral gt 17 Command Index 18 6 Command Index 6 1 Reading the initial configuration of system 6 1 1 Xml parser Constructor XmlReader const std string amp note specifies the XML file parser method parameter XML file name Example filename dppc xml sets the name of inputting XML file build method galamost XmlReader filename builds up the reading object of inputting XML file 6 1 2 Bin parser Constructor BinaryReader const std string amp note specifies the GALAMOST binary file parser method parameter binary file name Example filename initial bin sets the name of GALAMOST binary file build method galamost BinaryReader filename ffbuilds up the reading object of inputting GALAMOST binary file 6 2 Non bo
39. llInfo note specifies the dihedral opls cosine force parameter AllInfo Functions void setParams const std string amp Real Real Real Real Real note specifies the dihedral opls cosine force parameters parameters dihedral type Co C1 C2 C3 equilibrium dihedral degree Example dihedralforce galamost DihedralForceOplsCosine all info initializes DihedralForceOplsCosine object by AllInfo object dihedralforce setParams C_33 C_32 C_32 C_32 0 0 2 95188 0 566963 6 57940 0 0 Command Index 27 sets parameters by dihedral type Co C1 C2 C3 equilibrium dihedral degree app add dihedralforce adds this object to the application 6 4 Integration method 6 4 1 Nve ensemble Constructor Nve boost shared ptr AllInfo boost shared_ptr lt ParticleSet gt note specifies the NVE thermostat of a group of particles parameter AllInfo ParticleSet Functions void setZeroForce bool note switches the function of making all force to be zero parameters True or False the default is False Example thermo galamost Nve all_info group initializes Nve object by AllInfo object ParticleSet object app add thermo adds this object to the application 6 4 2 Nvt ensemble with Nose Hoover method Constructor NoseHooverNvt boost shared_ptr lt AllInfo gt boost shared_ptr lt ParticleSet gt boost shared_ptr lt ComputeInfo gt Real Real note specifies the NVT NoseHoover thermostat of a group of pa
40. nded forces 6 2 1 LJ force Constructor LjForce boost shared_ptr lt AllInfo gt boost shared_ptr lt NeighborList gt Real note specifies the LJ pair force Command Index 19 parameters AllInfo NeighborList cut off radius of interaction Functions void setParams const std string amp const std string amp Real Real Real note specifies the LJ interaction parameters by pair types parameters type 1 type 2 epsilon sigma alpha void setParams const std string amp const std string amp Real Real Real Real note specifies the LJ interaction parameters by pair types parameters type 1 type 2 epsilon sigma alpha cut off of radius void setEnergy shift note calls the function to shift LJ potential to be zero at the cut off point Example lj galamost LjForce all info neighbor list 3 0 initializes LjForce object by AllInfo object NeighborList object cut off lj setParams A A 1 0 1 0 1 0 sets parameters particle type 1 particle type 2 epsilon sigma alpha lj setEnergy shift shifts LJ potential to be zero at cut off app add lj adds this object to the application 6 2 2 DPD force Constructor DpdForce boost shared ptr AllInfo boost shared_ptr lt NeighborList gt Real Real unsigned int note specifies the DPD pair force parameters AllInfo NeighborList cut off of radius temperature RNG seed DpdForce boost shared ptr AllInfo boost shared_
41. nstallation and Usage 2 Installation and Usage 2 1 Compiling and installation The entire GALAMOST package is a Free Software under the GNU General Public License The package is mainly distributed as source code and binary program The binary program of full version and the code of simplified version can be downloaded from our website www galamost com The full version of code can be gotten by emailing to corresponding authors Here is the guide for installation by code Before compiling and installing of source code you should set configuration firstly i e installation path by following command configuration prefix opt galamost More configuration options are given here Commands Functions Examples prefix installation path prefix opt galamost cuda_arch Compute capability of GPU cuda_arch 20 precision precision format precision double gprof profiling tool gprof on gdb gdb tool gdb on After configuring a Makefile will be generated in current directory Then you can compile and install the package by the following command make install j4 where j indicates the number of threads to compile the code 2 2 Usage by script The C and CUDA C code has been written as an extended module of Python We can use the functions of GALAMOST by loading and calling its modules through a Python script Installation and Usage With the prepared script you should now be
42. oft anisotropic potential on the basis of the conservative potential in DPD It can be expressed as U 1 yt py y70 Af Iz 3 14 where the magnitude of a controls the strength of repulsion u controls the shape of the particles and v controls the angular width of repulsion The disk like or rod like particle can be described by different expressions of anisotropic factor f In disk like particle model the anisotropic factor is n r n f 3 ij 3 15 where n and n are unit vectors assigning the orientations to particles i and j respectively r r r is the interparticle vector In rod like particle model the anisotropic factor is f sin sin 6 3 16 where 0 is the angle between n and the interparticle vector r r ij gt 0 is the angle between nj and rj Characteristic Models 13 4 2 Polymerization model In this model we consider free radical linear chain growth polymerization that is mA gt A for monomer A Polymerization probability p is set to determine whether a monomer will react with an active end or not in a reaction step and is coupled to the real reaction rate r by ajm P P CSS a P dt d 3 17 where M is the free monomer concentration P is the concentration of growth centers and t is the reaction time interval In a time interval if a polymerization reaction event takes place between a monomer and an active end a bond connection should
43. ommand Index 53 note specifies the init of all kind particles parameters init void setInit std string unsigned int note specifies the init of the kind particle parameters particle type init void setInit unsigned int unsigned int note specifies the init of the particle parameters particle index init Example mol0 molgen Molecule 8 initializes Molecule object by the number of particles mol0 setParticleTypes A A A A A A A A sets particle types molO setTopology 0 1 0 3 0 4 2 3 1 2 1 5 2 6 3 7 4 5 4 7 5 6 6 7 sets topology mol0 setBondLength 0 75 sets bond length for all bonds mol0 setMass 1 0 sets mass for all particle mol0 setAngleDegree A A A 90 0 sets the degree of the angle of particles with the type 1 2 and 3 3 Objects defination Constructor Object unsigned int Object Shape note defines a object by Object parameters the number of particles in a molecule shape Object const std string amp unsigned int Object Shape note defines a object by Object and reads partial data from a file parameters file name number of particles in a molecule shape Functions void setBody Command Index 54 note specifies all particles in the molecule to be in the body parameters no void setBody std string note specifies the kind particle to be in the body parameters particle type void setBody unsigned int note specifies the particle to be in the body parameters parti
44. ortant informations Constructor ComputeInfo boost shared ptr AllInfo boost shared_ptr lt ParticleSet gt note specifies the method of dumping some important information Command Index 40 parameters AllInfo ParticleSet Functions void setNdof unsigned int note sets the freedom degree Example comp info galamost ComputelInfo all info group initializes ComputeInfo object by AllInfo object ParticleSet object 6 8 3 Sorting data Constructor ComputeInfo boost shared ptr AllInfo boost shared_ptr lt ParticleSet gt note specifies the method of dumping some important information parameters AllInfo ParticleSet Example sort method galamost Sort all info initializes Sort object by AllInfo object sort method setPeriod 300 sets computing period app add sort method adds this object to the application 6 8 4 VariantLinear Constructor VariantLinear note specifies linearly varing method Functions void setPoint unsigned int double note specifies the value at the time step parameters time step value Example v galamost VariantLinear initializes VariantLinear object Command Index 41 v setPoint 0 1 0 v setPoint 100000 2 0 set the value at the time step and the value at any time step can be gotten by linear interpolation 6 8 5 VariantSin Constructor VariantSin note specifies sinusoidal curve varing method Functions void setPoint unsigned int double
45. ptr lt NeighborList gt Real unsigned int note specifies the DPD pair force the defalt temperature is 1 0 parameters AllInfo NeighborList cut off of radius RNG seed Functions void setParams const std string amp const std string amp Real Real Command Index 20 note specifies the DPD interaction parameters by pair types parameters typel type2 alpha sigma void setT Real note specifies the temperature parameters a constant value of temperature void setT boost shared ptr Variant note specifies the temperature parameters a varing temperature according to time steps void setDPDVV note calls the function to enable DPDVV method the default is GWV V Example dpd galamost DpdForce all info neighbor list 1 0 12345 initializes DpdForce object by AllInfo object NeighborList object cut off RNG seed dpd setParams A A 25 0 3 0 sets parameters by particle type 1 particle type 2 alpha sigma app add dpd adds this object to the application 6 2 3 Pair force for LJ12 6 LJ9 6 harmonic Gauss Constructor PairForce boost shared_ptr lt AllInfo gt boost shared_ptr lt NeighborList gt note specifies the pair force parameters AllInfo NeighborList Functions void setParams const std string amp const std string amp Real Real Real Real Func note specifies the pair interaction type and parameters by pair types parameters typel type2 paramet
46. rete grid points of distance are given In the treatment of tabulated potentials the initial inputted potential tables on grid points of r are transformed to the tables arrays on grid points of z r With this trick the r SORT r in the inner loop of force calculation is avoided and the force is then calculated by OV r 1 M OV z Or r OZ F r 3 12 Within each interval between the grid points potentials are fitted to a cubic spline function more specifically for each x lt x lt x 4 let 0 x xj V x is represented by Force Fields 11 V 3X 2 0 6 6 0 3 13 where x corresponds to z 0 and for particle particle distance square bending angle and torsion angle respectively i is the index of the grid point and co is the starting potential value of each grid point Other parameters c c and c are chosen to make the values of the first derivative and the second derivative at both ends of interval x and x equal to the correct values of function V Characteristic Models 12 4 Characteristic Models 4 1 Soft anisotropic particle model By adding two degrees of freedom of rotation our one site anisotropic particle model can be used to describe disk like rod like diblock and triblock Janus particles We have successfully examined the packing and the self assembly of anisotropic particles with this model In the simulations of disk like and rod like particles we adopt a s
47. rticles parameter AllInfo ParticleSet ComputeInfo temperature tauT Functions void setT Real note specifies the temperature parameters a fixed value of temperature void setT boost shared_ptr lt Variant gt Command Index 28 note specifies the temperature parameters a defined varing temperature according to time steps Example nh galamost NoseHooverNvt all info group comp info 1 0 0 5 initializes NoseHooverNvt object by AllInfo object ParticleSet object ComputelInfo object temperature tauT app add nh adds this object to the application 6 4 3 Nvt ensemble with Berendsen method Constructor BerendsenNvt boost shared ptr AllInfo boost shared_ptr lt ParticleSet gt boost shared_ptr lt ComputeInfo gt Real Real mote specifies the NVT Berendsen thermostat of a group of particles parameter AllInfo ParticleSet ComputeInfo temperature tauT Functions void setT Real note specifies the temperature parameters a fixed value of temperature void setT boost shared ptr Variant note specifies the temperature parameters a defined varing temperature according to time steps 6 4 4 Nvt ensemble with Andersen method Constructor AndersenNvt boost shared_ptr lt AllInfo gt boost shared_ptr lt ParticleSet gt Real Real unsigned int note specifies the NVT Andersen thermostat of a group of particles parameter AllInfo ParticleSet temperature collision frequency RNG seed
48. rticles temperature pressure tauT tauP app add npt adds this object to the application 6 4 6 Nve rigid body thermostat Constructor NveRigid boost shared_ptr lt AllInfo gt boost shared_ptr lt ParticleSet gt note specifies the NVE thermostat of rigid bodies parameter AllInfo ParticleSet Example rigidnve galamost NveRigid all_info bgroup initializes NveRigid object by AllInfo object ParticleSet object app add rigidnve adds this object to the application 6 4 7 Nvt rigid body thermostat Constructor NveRigid boost shared_ptr lt AllInfo gt boost shared_ptr lt ParticleSet gt note specifies the NVE thermostat of rigid bodies parameter AllInfo ParticleSet Functions void setT Real note specifies the temperature parameters a fixed value of temperature void setT boost shared_ptr lt Variant gt note specifies the temperature parameters a defined varing temperature according to time steps Example rigidnvt galamost NvtRigid all_info bgroup 1 0 10 0 initializes NvtRigid object by AllInfo object ParticleSet object temperature tau Command Index 31 app add rigidnvt adds this object to the application 6 4 8 Brownian dynamic nvt rigid body thermostat Constructor BdNvtRigid boost shared_ptr lt AllInfo gt boost shared_ptr lt ParticleSet gt Real unsigned int note specifies the Brownian NVT thermostat of rigid bodies parameter AllInfo ParticleSet temperature R
49. s the following example non bonded DPD force NVT thermostat with GWVV algorithm and information analysis methods neighbor list galamost NeighborList all info 1 0 0 05 7 rcut rbuffer dpd galamost DpdForce all info neighbor list 1 0 12345 rcut seed dpd setParams A A 25 0 3 0 alpha sigma dpd setParams A B 40 0 3 0 alpha sigma dpd setParams B B 25 0 3 0 alpha sigma app add dpd group galamost ParticleSet all info all comp info galamost ComputeInfo all info group Gwvv galamost DpdGwvv all info group app add Gwvv dinfo galamost Dumplnfo all info comp info data log dinfo setPeriod 200 app add dinfo The tail of script usually sets the freedom degree for ComputeInfo method the number of time steps to run and the function of analysis of neighbor list etc comp info setNdof app getNdof app run 10000 neighbor list printStats Installation and Usage 2 3 Usage by user graphic interface 7 amp GALAMOST Fle Tool Simulation Help Chares Forces Thermostats Tinkers Dumps Modules NBonded Forces P LjForce Bond Forces IpdForce Angle Forces gt IpdThermoLjForce Dihedral Forces GravityForce nn LiWallForce PairForce Figure 2 1 The snapshot of UGI User graphic interface UGI can directly run and display on personal computer with Windows operation system and installed Python UGI also can run on remote workstation with
50. t AB CD gt AB CD grafting to Appended Documents 59 Reaction galamost Polymerization reaction setPr B C 0 005 reaction setMaxCris B 2 reaction setMaxCris C 2 reaction setPeriod 50 app add reaction TE xml h_cris B 1 h_cris C 1 h_init B 1 h_init C 0 4 ligand exchange B A C A B C reaction galamost Polymerization reaction setExchangePr B A C 0 1 app add reaction A C B DL 0 1 A C A B xml A A A C A h_init 1 B h_cris 0 CC h_cris gt 1 h_cris Ji 1 5 mobility iX A C ADA C A reaction galamost Polymerization reaction setExchangePr A C A 0 1 app add reaction C A BE DL 0 1 C A A C xml C C
51. tant Angle harmonic CI 6 3 4 Force Fields 9 1 angle angle 6 2 k p 6 Q y 3 7 Angle cosine harmonic CI 6 3 5 1 angle U ght 5 k cos 85 cos 8 3 8 Angle cosine CI 6 3 6 angle Ox gue 1 COS 8 A 3 9 in which 0 is the angle in radians between vectors r and rj 09 is the equilibrium angle and K is the angle force constant q g g Dihedral cosine CI 6 3 7 _ 7 dihedral U dihedral Pn k 1 COS Gu 3 10 Dihedral Opls CI 6 3 8 dihedral dihedral U jineara Piju K k 1 COS Pyu T 5 pan L ees 20 26 E p e E COS 395 30 3 11 Force Fields 10 in which Yin is the angle in radians between the planes i j k and j k l which pitihedral is drawed in Fig 3 1 6 is the phase shift angle and is the multiplicative constant EPP Pi Figure 3 1 The schematic diagram of jx 3 3 Numerical forces The numerical non bonded bond angle and torsion potentials can be derived from IBI or reverse Monte Carlo method With IBI method the procedure starts with the potentials of mean force as guessed potentials and then optimizes the potentials iteratively by mapping the structural distributions i e radial distribution function RDF onto the ones obtained either from atomistic simulations or from experiments The resulting numerical potentials usually take the form as a table in which the potential values at disc
52. time steps and direction parameters Variant and directional vector with x y and z void setParams const std string amp Real note specifies the factor multiplied by the external force parameters particle type factor Command Index 22 void setParams unsigned int Real note specifies the factor multiplied by the external force parameters particle index factor Example v galamost VariantSin v setPoint 0 1000 1 1 v setPoint 1000000 1000 1 1 set the parameters of sinesoid force by timestep period max and min value The latter three paramters are linearly varing by timestep groupA galamost ParticleSet all info A ef galamost ExternalForce all info groupA initializes ExternalForce object by AllInfo object ParticleSet object ef setForce v X sets parameters by force and direction app add ef adds this object to the application 6 3 Bonded forces 6 3 1 Bond harmonic force Constructor BondForceHarmonic boost shared_ptr lt AllInfo gt note specifies the harmonic bond force parameter AllInfo Functions void setParams const std string amp Real Real note specifies the harmonic bond interaction parameters of different types parameters bond type spring constant equilibrium length Example bondforce galamost BondForceHarmonic all_info initializes BondForceHarmonic object by AllInfo object bondforce setParams polymer 1250 000 0 470 Command Index 23

Download Pdf Manuals

Related Search

Related Contents

日本語  Assist Document  Food Handler Training - Online Presentation    RCA AVT-2050 User's Manual  Craftsman 79964 Chipper User Manual  Merlin Handbuch  HUMAX DVR 9950C  Samsung ML-1510 Manual de Usuario    

Copyright © All rights reserved. Failed to retrieve file